John McBain arrived in Llanview in October 2003. An FBI agent, posing as a billiard scout for crime lord Flynn Laurence, McBain used Natalie Buchanan and her fiancé Cristian Vega to get the goods on the crime lord. The way to do that was use Natalie's new found skills as a billiards champion. Unfortunately, Natalie defied John's orders to throw the game for Flynn and as a result she was kidnapped by Flynn. Although Cris and John were able to rescue Natalie, Cris apparently lost his life in the attempt. At first angry at John's indirect role in Cris' death, Natalie soon developed a friendship with him.
Very soon after, John decided to leave to FBI and began working for the Llanview PD, investigating a serial killer. What made John the perfect man to investigate this case was the fact that he was very familiar with this killer, dubbed the Music Box Killer, having investigated him years earlier. Although John had not been able to catch the killer then, he taunted him so sufficiently that the murderer targeted John's lover, Caitlin Fitzgerald. After Natalie was nearly murdered by the Music Box Killer, she and John finally admitted that their friendship was turning into something more. John eventually apprehended Dr. Stephen Haver and brought him to justice as the killer.
Just as Natalie and John's relationship seemed to be getting stronger, Kathryn Fitzgerald, the sister of John's dead fiancée Caitlin, came to town. Kathryn had also been an FBI agent and confessed to John that she had always cared for him. John didn't feel the same way, so the feelings went nowhere. But jealous of the connection between Kathryn and John, Natalie began spending more time with Paul Cramer. Natalie and John again confronted their feelings for each other and the two nearly made love, but John wasn't yet over Caitlin. Natalie then began seeing Paul. After tying Paul Cramer to the Santi family crime family, Kathryn was soon out of the picture when she was found murdered in Evangeline Williamson's office. After another of Evangeline's clients was found murdered, she and John began working on the mystery together, which soon brought them closer together.
Natalie ended things with Paul long before it got truly serious, and began falling back for John, who by this time was with Evangeline. Just as Natalie was making an active play for John, Cristian showed up back in her life again, alive and well. As Evangeline and John grew closer, the reappearance of Cristian Vega only served to remind John that he still cared about Natalie. Convinced that Cristian was an imposter, he investigated him thoroughly, and it wasn't long before he was able to arrest Cristian for Tico Santi's murder. John received a shock when DNA tests came in proving that the man was no imposter and was in fact the real Cristian Vega, but Cristian begged John to keep it secret, not wanting Natalie and his family to realize what he had become. He kept the secret and continued his relationship with Evangeline, but his feelings toward Natalie remained strong.
Natalie and John finally began a romance, but it was short-lived. During the Statesville prison riot, Natalie learned that the man she believed was Cristian's imposter was in fact Cristian himself and, making matters worse, John had known all along. Natalie was furious with both men for lying to her and making her an adulteress. She immediately demanded a divorce from Cristian and attempted to cut John out of her life.
Over the course of 2006, however, Natalie reunited with John after working with him to prove her uncle Todd Manning innocent of the "murder" of Margaret Cochran, and helping him finger Spencer Truman as the man who killed John's father. Natalie took a job as receptionist for the Llanview Police Department and soon showed an interest in the forensics program. Working closely with John, her relationship with him deepened; Natalie began to hope for marriage. But after a horrifying car accident in which John was badly burned and thought dead, Natalie's bond with John began to fray. He became volatile and verbally abusive, unwilling to communicate. Thinking she was protecting John, Natalie tampered with evidence at the crime scene of Spencer Truman's murder; when the truth came out, she was dismissed from the forensics program. Her relationship with John disintegrated as well, but they ultimately parted as friends, with John admitting he should have treated her better.
After Truman was murdered, psychiatrist Marty Saybrooke began having flashbacks of blood and a scalpel in the hospital room where Truman was murdered and was convinced she was the killer. While in therapy, she admitted her belief that she had killed him and Miles Laurence, who was obsessed with Marty, obtained her confession on tape and blackmailed Marty into marriage. John, who had become friends with Marty, detected that something was wrong and eventually got Marty to admit that she believed she had killed Truman. Marty was arrested for the murder, but John continued to uncover the facts and eventually found conclusive evidence that led to Lindsay Rappaport as the real murderer.
After being cleared of murder, Marty annulled her marriage to Miles and continued to get close to John. Their friendship soon blossomed into love. But in the fall of 2007, Marty and her son Cole were abducted by Simon Ryerson, a former friend of Marty's dead husband Patrick Thornhart. Simon, it turned out, had actually killed Patrick. He held Marty and Cole captive in Ireland and threatened to kill Cole if Marty didn't hand over Patrick's list of names of the Men of 21. Marty was unaware that the list had been hidden on a microchip in a book Patrick had given to her. John began searching for Marty and Cole and at her apartment found the book with the microchip. He and FBI agent Lee Ramsey flew to Ireland and contacted Simon with plans to exchange Marty and Cole for the microchip. An impatient Ramsey fired shots into the van holding Marty and Cole and the van rolled down a cliff into a quarry. John raced to the scene and found Marty alive but Cole missing. He struggled to free Marty from the wreckage but she insisted that he first locate Cole. Thrown from the van, Cole was seriously injured but alive. As John returned to rescue Marty the van exploded and Marty was presumed dead. John and Cole returned to Llanview, where Cole was taken in by Nora Buchanan and turned to John for friendship.
In the spring of 2008, John became suspicious about Ramsey's shady activities since he became Police Commissioner of Llanview. Banding together with fellow police officers Antonio Vega and Talia Sahid, John worked to expose Ramsey as a dirty cop and avenge Marty's death. During the course of their investigation, the trio learned about a mysterious woman Ramsey was keeping hidden away in his high-rise penthouse, tended to by a private nurse named Janet Ketring. John became convinced the woman was the key to unraveling the mystery behind Ramsey's double dealings. John was correct: Ramsey masterminded the theft of the crown jewels of Mendorra from Lindsay Rappaport's art gallery in order to fence them and pay for his houseguest's costly medical care. Ramsey's mystery woman not only was bedridden but also mentally impaired. John discovered X-rays in Ramsey's office that detailed the severe physical trauma of an unidentified female patient.
John had a surveillance device planted inside Ramsey's penthouse. John, Antonio, and Talia staked out the building, waiting for Ramsey or his guest to come into audio range of their "bug." On June 11, 2008, the officers listened in as Ramsey spoke to the woman, who said only two words on tape before the surveillance device went out of range: "Help me." John struggled to identify the familiar voice, but he was unable to figure out that the mystery woman being cared for by Lee Ramsey was none other than Marty.
During a botched attempt to fence the stolen jewels, Ramsey was shot dead in his apartment. Todd Manning showed up and found a very-much-alive Marty upstairs. Realizing Marty had no idea who he was, Todd whisked her away to his new home and began nursing her back to health - all the while filling Marty's head with lies about how evil John was and how he had left her to die in Ireland. In several dreams, Marty had interactions with John, who urged her to question Todd's motives. But Todd managed to convince Marty that the dreams were not reality and that she should fear for her safety from John. John, meanwhile, found himself in a relationship with Todd's ex-wife Blair Cramer.
After months of failed attempts to figure out who Todd was keeping in his home, John obtained definitive proof from Todd's old bodyguard that Marty was the woman being cared for in Todd's home. A judge denied John a warrant to search Todd's home, however, so John broke into the home while Todd was away and found a shocked Marty. John told Marty that Todd had lied to her and that he was the one who had raped her in college. When Todd showed up, he admitted to Marty that it was all true. Marty was sick to her stomach, since just hours before she and Todd had made love for the first time since that fateful incident. When John learned this, he beat Todd to a pulp. Marty held a gun on Todd and considered shooting him, but John convinced her to let the authorities deal with Todd.
John found himself in trouble with the mayor after word came out about his role in freeing Marty. He resigned from the force but was given his old job back after embarrassing the mayor on live television, only to turn around and resign again anyway. John tried to be a friend to Marty, who was having a difficult time adjusting to life outside of Todd's orbit, but he was also trying to maintain a romantic relationship with Blair. Although Blair tried hard to be understanding about what Marty had been through, jealousy soon reared its ugly head and Blair felt threatened by the attention John was paying to Marty. John offered to take Blair away for a quiet vacation on St. Blaze's, the island once owned by Asa Buchanan, but Blair said she couldn't leave her family behind. She and John planned a romantic evening for New Year's Eve at Rodi's Tavern, which John had just purchased, but then John was called away by Cole after Marty turned up missing. Marty had begun to research everything about Todd's life, and John figured out that she was planning to lure Todd into some sort of trap. He tracked Marty down at the Palace Hotel, where she had booked a room, but neither Marty nor Todd where there. When a man jumped from the roof of the hotel and fell into the river below, John jumped in and pulled the man to safety, only to discover it was Todd. Marty, who had goaded Todd into jumping from the roof, hissed at John for rescuing him. Blair meanwhile was forced to defend herself to John for reviving Todd and being grateful that Todd had not died.
Marty found a new friend in Wes Granger, a former Navy SEAL who was staying at the Angel Square Hotel. John felt Wes was a bad influence on Marty, who had begun reverting to her old ways and drinking too much, and had words with the younger man. Then he found out that Wes had just gotten a job at Rodi's working for John. John allowed Wes to keep his job, but it seemed that he was only interested in keeping an eye on Wes and Marty. Marty confessed to John that she was drawn to him but didn't want to get closer to him, and John responded by telling Marty to "forget about Blair." Blair overheard the conversation and later told Marty to back off.
Janet Ketring, the woman who had helped nurse Marty back to health, was found murdered in Todd's home. John noticed that Wes took a keen interest in the story. He did some research and learned that Wes' family had been taken for everything they had by Janet, back when she was known as Lee Halpern, and suspected that Wes may have killed the woman. John took Blair to the Go Red Ball but after a melee between Todd and Wes, who took out a knife and held it to Todd's throat, John publicly accused Wes of killing Janet. The next morning, John burst into Wes' hotel room after hearing Marty screaming and discovered a blood-soaked Marty lying in the bed beside Wes, who had been stabbed to death with his own knife. Marty said she didn't remember what had happened, and John believed her and was reluctant to call the cops. But when Blair walked in on the scene, she called the cops and Marty was taken into custody and arrested for the murder.
When Blair later found John back at the scene of the crime, searching for anything that could free Marty, Blair told him that he was still in love with Marty and broke up with him. Blair later called the sleazy tabloid, The National Intruder, and provided them a photo of a blood-soaked Marty that she had taken with her cell phone. John was livid to learn what Blair had done and had it out with her, but their anger turned to passion and they ended up in bed, ready to make love. They were interrupted by Marty, who called John's cell phone because she was worried about Cole, whom she had discovered was abusing drugs and flunking out of school. John went after Marty, and Blair told him to not ever come back; soon after, she was stabbed and nearly killed by an unknown assailant. While John and Marty were out searching for Cole, they heard a car accident and were shocked to discover that Cole had wrecked his car and nearly hit Gigi Morasco and her son Shane. Blair survived her attack, but John blamed himself for not being there to keep her from being attacked. When Blair's attorney Téa suggested that Blair marry John so Todd couldn't get custody of their kids, John agreed to marry Blair.
Police thought they had found their serial killer after one of Marty's former attackers, Zach Rosen, showed up in town and took Starr and Cole hostage after Todd refused to give him money. But when Police Officer Talia Sahid was found stabbed to death by John at La Boulaie, while Zach was still in custody, it was clear that the attacker was still out there. John was arrested after authorities found the knife used to stab Blair in his apartment, with his fingerprints on it. John escaped jail and realized Marty was the next target after finding a picture of Marty in his apartment with a knife through it. John went to Marty and warned her to be safe, but Marty said she was going to go with John to find out the truth. They ended up outside Rochester, New York, where Marty's third attacker, Powell Lord, was being held in a sanitarium. Using false names, Marty and John got in to see Powell. Powell pretended that he didn't remember Marty, but in fact he was colluding with one-time love Rebecca Lewis to get back at Todd. Rebecca was even posing as Marty so she could get access to the sanitarium. When John returned to the sanitarium to see Powell, he found an administrator dead and Powell gone and soon was locked in the room by Rebecca. Marty, Todd, Blair and Téa all succumbed to poison invitations sent by Powell and Rebecca and woke up at the KAD house, where Powell had reconstructed the room in which Marty was raped in a twisted attempt to make Todd pay for his crimes. John managed to escape from the sanitarium and burst into the room just as Powell was about to kill Todd, and he shot Powell dead. As John went to rescue Blair and Téa, who were locked in the boiler room downstairs, Rebecca appeared and lit a match, causing the place to blow up. Rebecca was killed and Téa was seriously injured but survived.
Marty told John that during the ordeal at the KAD house, her memories had come back to her. Wanting to explore a relationship with Marty, John asked Blair for a divorce and she agreed. But the memories of being with Todd haunted Marty, and she was unable to make love to John. When Cole Thornhart was arrested on drug possession, John managed to keep Cole from doing time by agreeing to return to the police force in exchange for being able to use Cole in a sting operation intended to find out who was supplying Llanview's youths with drugs. Marty was petrified for his safety, but realized that Cole was in less danger with John watching over him than he would be in Statesville Prison. To further aid the effort, John recruited Brody Lovett to go undercover as well and help expose the drug runners. Cole quickly established himself with the drug dealers, and his successful undercover work helped John discover that Mayor Stanley Lowell was behind the drug smuggling operation. Cole's cover was blown after Todd saw Cole selling drugs to Justin Lowell, the mayor's son, and Starr was forced to tell her father that Cole was working undercover. Dorian overheard the conversation and told Mayor Lowell, who put out a hit on Cole. Todd also went to the mayor, asking him to fire John because of the danger he had put his daughter and granddaughter in. Cole was nearly killed by a dirty cop, but John killed the cop first. After the botched attempt to kill Cole, Lowell told Serge to kidnap Starr and baby Hope and then was arrested after being exposed by John. Shaun Evans tried to stop the kidnappers and was shot multiple times, while Todd was severely beaten up. Starr and Hope were held in a warehouse but eventually escaped unharmed thanks to a rescue operation headed by undercover officer Brody Lovett.
John and Marty made love for the first time since her accident and subsequent rescue, but then John found himself drawn back into Natalie's orbit when her husband Jared was named the prime suspect in two murders that were tied to the stalking of her sister Jessica. Natalie believed John was out to prove Jared was guilty and, when Jared went missing, set out to find Jared before John could. The search led them to Nash Brennan's old vineyard in Napa Valley, where it turned out that Mitch Laurence was behind everything that had transpired. John and Brody closed in and prepared to ambush Mitch, but Mitch got the upper hand and shot Jared dead. Natalie lashed out at John afterwards, but John helped her grieve for her lost husband. When Natalie stabbed Mitch while John's back was turned, John planted evidence to make it look like Mitch stabbed himself. Mitch vowed revenge on John and Natalie and named John as the person who stabbed him. Natalie admitted to Bo and Nora that she had stabbed Mitch, but after Dorian forced Bo to resign as police commissioner on orders from Mitch, Nora presented evidence that pointed the finger at other suspects, forcing new police commissioner Stanley Lowell to drop the charges against John and drop the case entirely.
After Mitch Laurence lured Brody to the docks and began taunting him about Jessica, Brody nearly killed Mitch until John appeared. When the police arrived, John took the fall for the assault so Brody could escape. After a judge ordered John held without bail on charges of assaulting Mitch, Brody overtook a guard outside the courtroom and barged in to the courtroom with his gun drawn, threatening to shoot Police Commissioner Stanley Lowell if he didn't give up Mitch's whereabouts. Lowell hid behind John as Brody fired; John took the bullet, although it was all an elaborate ruse to break John out of custody. Brody broke free of the police officers who had apprehended him and joined John outside, where the two got into a getaway van driven by Natalie. Marty lashed out at John for scaring her nearly to death. The trio were searching for the whereabouts of Mitch, who had kidnapped Jessica, when they ran off the icy road. Brody headed off to search on foot while John freed Natalie, who was pinned beneath the steering wheel, just moments before the van exploded. Natalie and John found shelter in a cabin. Natalie believed that John was her dead husband Jared and John went along with it, even to the point of kissing Natalie and telling her that he loved her. When Natalie later came to, she realized what John had done and John admitted he still had feelings for her. They began kissing again when Marty showed up, having walked a mile in the snow to find them. Marty expressed her anger at John and refused to give John an answer when he asked if she still wanted him in her life.
John and Natalie tried to stay away from each other, but they shared another passionate kiss at Llanfair. John indicated to Natalie that he didn't want to give her up. Later, Natalie congratulated John for getting Marty pregnant, unaware that Marty hadn't yet told him. John told Natalie he was moving Marty into his apartment because Marty's pregnancy was considered high risk, and Natalie vowed not to get in the way. John went to California with Kelly Cramer to help her investigate the mysterious death of her mother, Melinda, and they met a fellow sanitarium patient named Rodney who seemed to know something about Melinda's death. When John returned to Llanview, he found Marty unconscious at the bottom of a hospital stairwell. John and Marty were heartbroken to learn that Marty had lost the baby. Marty told John that someone had pushed her and pointed the finger at Natalie, telling John that she and Natalie had gotten into a heated argument and Natalie claimed John would be with her if not for the baby. John questioned Natalie, who denied it and couldn't believe John would consider her. Then Marty recalled having gotten in an argument with Todd before her fall, causing John to turn his suspicions to Todd. When Cole's friend Hannah O'Connor claimed to have seen Todd push Marty, John arrested Todd for the crime. Todd claimed Hannah may have pushed Marty herself, to drive a wedge between Cole and Starr.
Marty struggled to cope with losing the baby. John suggested they try again, but Marty said it was too soon to consider that. John was surprised when Marty presented him with a letter from Natalie that she had intercepted; in the letter, Natalie told John she was moving to London unless he met her at Rodi's that night. Marty told John she didn't want to stand in the way of John and Natalie being together and broke up with John. John raced to the airport and found Natalie, professing his love to her.
In his professional life, John soon found himself dealing with a spate of crimes. Mental patient Rodney died of an apparent heart attack after traveling to Llanview to tell Kelly who had murdered her mother. Kelly later found a slip of paper inside a vase her mother had given her containing the name Bennett Thompson and told John she was sure this man was behind her mother's death. In May 2010, Robert Ford was attacked and nearly killed while lying in his bed. Ford named Hannah as his attacker, and John found evidence in Hannah's dorm room linking her not only to Ford's attack but to Marty's crime as well. Hannah admitted she lied about seeing Todd push Marty down the stairs, but she denied attacking Ford and Marty. After a brief conversation with her attorney, Eli Clarke, Hannah seemingly had a mental breakdown and confessed to both crimes. Eli denied having coerced his client into faking a mental breakdown, but John remained suspicious. When Rex Balsom was drugged in Boston while searching for clues into Bennett's identity, evidence pointed to a man matching Eli's description. But John was unable to confirm the story because the man who had seen Eli died an apparent heart attack before he could ID him. John thought he caught a break when Layla mentioned that her mother had contacted Bennett Thompson for legal advice concerning Evangeline's living will and that Evangeline had a file with Bennett Thompson's name on it. But Eli got to the file before John could retrieve it.
Natalie told John she was pregnant and John agreed not to say anything after Natalie said she didn't want to jinx the pregnancy. John had no way of knowing that Natalie was worried the baby might be Brody's instead of John's.
After Hannah overdosed on pills while in St. Anne's, she admitted to John that Eli had threatened to hurt Cole if she didn't comply and tipped off John that Ford knew more than he was saying. Ford admitted that he had blackmailed Eli with the knowledge that Eli's alias was Bennett Thompson. Ford had had an affair with Bennett's wife, Olivia, while he was living in Los Angeles a few years earlier. Olivia was very rich and told Ford that her husband had married her for her money. Soon after, Olivia disappeared and Ford assumed she had skipped town after her husband found out about their affair. Ford told John that he has falsely accused Hannah O'Connor of bludgeoning him because Eli had threatened his family.
John got another clue when Kelly presented him with a mug shot of Eli, which the police traced to yet another alias, Craig Pattison, who had been arrested on suspicion of murdering his wife. The evidence was enough to get an arrest warrant for Eli, who had fled to Tahiti with Blair. John flew to Tahiti after Kelly admitted that she had reached Blair and had told her all about Eli. John arrived to find Ross Rayburn's cabana on fire, with Blair and Eli inside. John got Blair to safety but was unable to rescue Eli, who was trapped under fallen debris. At the police station, Blair identified Eli's badly charred body, although she admitted to John that Eli was so badly burned he was unrecognizable. The cops presented John with the bullet that had been taken from Eli's stomach and the wedding photo of Eli and Blair, which was pulled from his pocket. Eli appeared dead, although John asked for more evidence before he would close the case.
The DNA on the dead body was corrupted, and John grew suspicious that Eli had staged his death, likely with help from his brother Ross. Ross soon showed up in Llanview, claiming that Téa Delgado had changed her will to give him custody of Danielle shortly before she died. John was on the verge of getting Ross to admit that Eli had staged his death but then Ross was summoned to court, where a judge awarded him full custody of Dani based largely on Dr. Greg Evans' testimony that Téa had wanted Ross to have Dani. John realized that Greg seemed to be in cahoots with Ross and Eli and flew to the hospice on St. Kitts where Téa had died. There John found Greg unconscious, having been injected with a near-lethal dose of morphine, and Eli was nowhere to be found.
Back in Llanview, Eli resurfaced and, after shooting his brother dead, kidnapped Starr, Hope and Dani. John learned from Natalie that Téa was alive, but without definitive proof he decided not to tell Todd. Eli demanded $50 million from Todd in exchange for the girls, and the hostage situation came to a head at an abandoned warehouse. After Eli had freed Dani, he set off an explosion inside the warehouse. John raced inside, along with Todd, and they ended up getting trapped in a tunnel beneath the warehouse when the roof collapsed. John told Todd that Téa was alive and could have been in the warehouse when Eli set off the explosion. John was relieved when they rescued Blair and Téa and made their way to safety.
John was suspicious when Marty confessed to having murdered Eli in retaliation for killing their unborn child and kidnapping Starr and Hope. When he questioned Natalie about the forensic evidenced, she had no choice but to admit that Marty hadn't fired the gun and Cole's fingerprint was found on the trigger. Marty pleaded with John to let Cole go, but John said he couldn't ignore the evidence because Natalie could go to jail if the truth ever came out. Cole eventually turned himself in, and after pleading guilty to second degree murder he was sentenced to 10 years at Statesville Prison.
Marty began planting seeds of doubt in John's mind regarding Natalie's honesty. After Natalie had told John she had gone to the hospital to get vitamins, Marty revealed to John that she had actually gone there to have an amniocentesis performed. John confronted Natalie, who said she got the procedure done because she was worried what would happen if something happened to the baby since John had already lost one child. John forgave Natalie for keeping the appointment a secret from him, but told her she needed to be honest with him going forward. Later, Marty confronted Natalie and John with a copy of Natalie's medical file regarding the amniocentesis, which Marty said proved Natalie was a liar. But John refused to look at the document, telling Marty he already had already talked to Natalie about it. John told Marty she needed to stop blaming Natalie for Cole going to jail.
After Cole got into a fight at Statesville, John called in a favor to the prison warden and had Cole transferred to a different cell block. Marty was grateful for John's kindness, but John could still tell that she was having a hard time coping with Cole's incarceration. After Natalie's brother Joey returned home for Thanksgiving and announced he was engaged to be married, John decided to pop the question to Natalie and she said yes on Dec. 13, 2010. With Joey and Jessica planning to marry in the new year, John suggested that he and Natalie marry quickly. They secured a courtroom and judge on New Year's Eve and, with Jessica and Brody serving as witnesses, exchanged vows as fireworks exploded in the distance signaling the start to 2011. But moments before the judge could declare them married, Marty interrupted the ceremony claiming to have something important to tell Jessica. Jessica began having labor pains and had to go to the hospital before Marty could say anything, however. John accompanied Brody and Jessica to the hospital, leaving Natalie with Marty. After failing to reach Natalie for hours, John tracked her down at the Buchanan lodge thanks to the tracking device in her vehicle. He got to the lodge to discover that Natalie had gone into premature labor and was giving birth with Marty's help.
John was overjoyed when Marty presented John with his healthy baby boy, but John and Natalie quickly realized that Marty had suffered a psychotic breakdown when she believed that the boy was actually the son she and John had lost nearly a year earlier. Natalie told John that Marty had forced her to drive to the lodge and had held her at gunpoint. At the hospital, Marty broke free from the restraints and tried to take off with Natalie's baby, but John intervened and got the baby from her. Marty was taken to St. Anne's for treatment. John and Natalie named their baby Liam Asa, while Jessica and Brody named their own newborn boy Ryder Asa. John learned from Bo that Clint had orchestrated the breakup of Bo and Nora's marriage and was behind Nora's kidnapping by Eddie Ford and possibly Eddie's murder. John kept the news from Natalie until Bo could get evidence to convict Clint.
John and Natalie prepared to marry on Valentine's Day in a double wedding ceremony with Brody and Jessica. On the day of the wedding, Marty showed up at John's apartment, having recalled that their baby actually had died. Marty said she knew something about Natalie and Brody but couldn't remember what. Marty was distressed when she was taken back to St. Anne's, leaving John with suspicions about what Marty knew. Before the couples could exchange vows, one of Clint Buchanan's employees interrupted the wedding and announced that he had changed the paternity tests for one of Clint's daughters. The test that was changed was Jessica's, meaning that Ford was the father of her baby, not Brody. When John realized that Natalie had a paternity test too, he demanded the truth and forced Natalie to admit that Liam was the result of a one-night stand with Brody. Natalie begged for forgiveness, but John walked out on her. John proceeded to get very drunk at Rodi's with Kelly, who was also in despair after watching Joey marry Aubrey. The two got into a bar fight at a dive bar on the outskirts of town and ended up in a room at the Minute Man Motel, where they had sex. The next morning, Kelly tried to convince John that he still loved Natalie but John wanted to hear none of it. Natalie showed up and saw Kelly coming out of the shower, and John acknowledged that he and Kelly had had sex. Natalie was livid, but John told her they were through and that he couldn't trust her ever again.
When Joey learned that John and Kelly had had sex, Joey ordered John not to lay a finger on Kelly and then punched John in the face after John remarked that he had laid "more than a finger" on her. John and Kelly continued to console each other and began sleeping together regularly. John visited Marty at St. Anne's and Marty acknowledged she had hoped to use the paternity test results to hurt Natalie. But Marty said she knew what she had done was wrong, and with John's help Marty was released from St. Anne's. Natalie discovered that John still had one of Liam's sonograms and angrily ripped it up, telling him that he could come over and see Liam in person instead of looking at a photograph. Natalie then returned her engagement ring, telling John that they were over.
John and Todd were caught in the crossfire outside Rodi's when someone took aim at Todd. Todd was shot and went into a coma. Natalie found a Euro at the crime scene, and John became suspicious of Téa's brother Tomas after learning that he had recently arrived from Paris and had already had words with Todd. John warned Blair to be on her guard around Tomas and ordered a deputy to do a thorough background check on Tomas. John discovered that the CIA had a confidential file on Tomas - just like one on Todd Manning that Kelly and Blair found in Todd's office. When Todd awoke from his coma, he named Tomas as his shooter and John had Tomas arrested. John later was forced to release Tomas after Todd recanted his claim.
Kelly told John that Marty had threatened to hurt her if she didn't break things off with John. John pretended to still be interested in Marty, but he quickly realized that she was obsessed with him. John went to his apartment and found Kelly in the bathroom, near-death from multiple stab wounds. Kelly told John that Marty had attacked her. He went back to the hotel and found Natalie on the ground, having been pushed off the roof by Marty. Marty knocked out Brody and stole his gun, running off with Liam. John told Natalie that she had called him just before going over to his apartment, saying she had something urgent to tell him, but Natalie couldn't remember what it was. Brody got a tip from Jessica's alter, Bess, that Todd was the key to finding Liam. John got a warrant to search the Manning home and found Tomas in the pool house with Liam. Tomas claimed to have just found Liam there. John tracked down Todd to a private airstrip, where Marty had just taken off on a plane to an unknown destination. Todd claimed he had followed Marty from his home to the airstrip but had nothing to do with her getaway.
John got called into another crime when an unidentified man was found dead on the grounds of Dorian's home. John found an encrypted CIA on the man, just like the ones on Tomas and Todd. All of the files shared the same mysterious symbol that John was unable to identify. John questioned young Sam Manning about the murder after Blair said Sam claimed to have met a man with a line on his face near where the murder occurred. Sam told John that his friend had saved his life and he identified his friend from a picture of Todd with his original face. Sam later was abducted by a man wearing a Spiderman outfit, and the man who originally was wearing the outfit identified his assailant from a picture of Todd with his original face. Sam was found unharmed and claimed that the man who had taken him was a friend. John got a call from the man with Todd Manning's original face and met him at the docks, where the man claimed to be Todd Manning. John protected the man from sniper fire. He took the man claiming to be Todd back to his apartment, where the man explained how he had escaped from an unknown location after being held captive for eight years. John took a DNA sample from the man and then snuck into Todd's office at The Sun to retrieve Todd's toothbrush. Tomas told John that he was a former CIA agent who had worked for a man named Malcolm Baker who was behind Todd's shooting several months earlier. John urged Tomas to come clean about what Baker wanted and why he was a threat to Todd and his family. Just as Tomas told the Manning family that the man they knew as Todd was an imposter, the man with Todd's original face appeared and claimed to be the real Todd Manning. John intervened and took the man with Todd's original face into custody after he pointed a gun at Todd. The next day, John revealed the results of the DNA tests, which showed that both men were a match for Todd Manning.
John tracked Agent Baker to a secret facility in Louisiana where Todd had been kept prisoner and conducted a raid on the facility with help from Tomas and police officer Brody Lovett. There they discovered the mastermind of the rogue CIA operation, who turned out to be Todd's believed-dead mother Irene Manning. They brought Irene back to Llanview, where she revealed that the man who had recently returned to town was in fact Todd, while the other man was Todd's twin brother Victor Jr. Irene had been holding Todd captive for years and had brainwashed her other son into thinking he was actually Todd. Soon thereafter, Victor Jr. was found shot and pronounced dead. Jack had been brought to the hospital unconscious around the time Victor was killed, and Jack pointed the finger at Todd. John arrested Todd for the crime, but Téa insisted that Todd was innocent. Todd escaped from jail and shot and killed Irene during an encounter on the docks. When John showed up he found Tomas, who confessed to the crime so Todd could escape. Tomas was sentenced to 20 years in prison but the conviction was overturned when Todd confessed.
John, meanwhile, was disappointed when he heard that Natalie and Brody were getting married but he refused to tell Natalie that he still loved her. John quit the police force and was about to board a flight to Seattle to visit his brother Michael and sister-in-law Marcie when Natalie showed up in her wedding gown and announced that John was Liam's father. Marty had switched the DNA test results and Brody had kept quiet after hearing Marty's confession on a tape that was found with Gigi Morasco's unconscious body. The truth came out at Natalie and Brody's wedding, when Tina presented Natalie with the real results. John was overjoyed and they went to Llanfair to see Liam, only to discover that Brody had knocked out Nigel and kidnapped the baby. John and Natalie tracked Brody down at his family's home in Michigan, and Brody agreed to return the baby. John was happy to be a father, but Natalie refused to forgive him for failing to admit that he still loved her and not stopping her wedding to Brody. After Gigi turned up alive, John and Natalie realized that they were squabbling over nothing and the two shared a long-overdue reunion.
When the police investigation into Victor's murder hit a dead end, Tomas told Téa that he would find out who killed Victor. But Tomas soon went missing and John found the gun used to murder Todd hidden in Tomas' room. Téa worked with John McBain to clear Tomas and the two came to believe that Todd was in fact the guilty party. After Tomas confessed to the murder during a live phone chat with Blair, Téa and John tricked Tomas' friend Claude into revealing that Tomas was being held against his will. John stole Todd's phone and planted a bug that led him to Tomas. As Tomas and Téa reunited, John promptly arrested Todd for the murder of his brother - unaware that Victor Jr. was very much alive and being held captive by Allison Perkins.
In March 2012, John arrived in Port Charles, New York, on the trail of Todd Manning, who had skipped bail after learning that his daughter Starr had been involved in a car accident there. John tracked down Todd at the courthouse, where Todd was pointing a loaded gun on Sonny Corinthos, the man Todd believed had caused the accident that killed Todd's daughter's fiancé Cole Thornhart and their daughter Hope Manning. John fired a warning shot to make Todd drop his weapon and promptly took him into custody so that he could bring Todd back to Llanview to face murder charges. Before he left, John confronted Sonny, whom John had tried but failed to collar while working at the FBI. John warned Sonny that if Sonny had anything to do with the accident, he would return to Port Charles to make Sonny pay.
John admitted that his father on his deathbed had told John that he had a half-sister, Theresa, born as the result of an affair. John had spent ten years tracking down Theresa, discovered that she had fallen in with organized crime, and was involved with Sonny who gotten her killed.
After the warrant John had to investigate Sonny expired and John had to return to Llanview, he finally let Sonny tell his side of the story. Sonny said that when they were in high school, Kate and Sonny planned to run away together. Kate was going to college, and Sonny had a legitimate job. But Kate never showed up, so when mobster Joe Scully offered him a job, Sonny ended up running a club in Atlantic City. Later Joe set up his son, Joe Jr. in Atlantic City where Theresa worked as a dancer, but Joe Jr. didn’t know she was underage. After John had located her there, Theresa had told John that she could not leave the club or her boss would kill her. Sonny said that Joe Jr. wanted Theresa. One day Sonny heard her yelling, and saw that Joe Jr. had her by the hair. Sonny tried to get him to let her go, but instead Joe Jr. shot her, dropped gun, and ran. Sonny swore it was the truth. John had gotten there in time to find Sonny kneeling over her body with the gun, trying to help her, so John arrested Sonny for murder. Sonny swore it was the truth. When asked by John, Sonny said that Joe Jr.’s father paid off the police to get his son out of trouble, and last he heard Joe Jr. had gone to New Orleans. McBain appeared to believe Sonny, and left for Llanview, Natalie, and their son Liam.
Instead, John went to New Orleans in search of Joe Jr. Jason was also on the same mission and the men were seated next to one another on the plane. John arranged for Jason to be detained on the plane so he would have a head start in locating Joe Jr. John did reach Joe Jr. first and informed him that he was headed to Atlantic City to stand trial for the murder of John's sister Theresa. As John handcuffed Joe Jr. some of his associates entered and clobbered John over the head and tied him up. Jason arrived as Joe Jr. delivered orders regarding what to do with John and killed Joe Jr.'s thugs. Jason took off with Joe Jr. but he left John behind tied to a chair.
When John returned to Port Charles, he found Joe Jr. being held by Sonny. The men questioned Joe Jr. at gunpoint regarding the crimes he had committed. Joe Jr. admitted that he had killed Theresa but claimed that her death was on John's hands since he had killed Theresa after he saw her talking with a federal agent. John was the agent that Theresa had been seen with. After Joe Jr. confessed, the police arrived and transported him to a prison cell in Atlantic City.
After Joe Jr.'s accusation that John was responsible for Theresa's death, John was consumed with guilt and he turned to alcohol for comfort. Sam found him and they shared a kiss. Afterward they admitted that they shared a connection but it would not go anywhere because they were both in love with other people. They parted ways unaware that Heather Webber had photographed their kiss and given it to her boss Todd.
Todd still blamed John for his most recent break-up with Blair since John had arrested him for murdering his brother Victor. Todd mailed the picture of the kiss to Natalie. When John returned home to Llanview, he found the picture and discovered that Natalie had taken their son and left him. John returned to Port Charles and took his anger out on Todd in a physical way. Afterward Todd filed assault charges against him and John was arrested. Sam arranged for her mother, Alexis Davis, to be his legal counsel. Alexis recommended that John obtain employment in order to strengthen his case for paternal rights. He followed her advice and took a position as a police officer with the Port Charles police department.
Shortly after John started his new position, he was stabbed in the chest by a former resident of Port Charles named Lucy Coe. Lucy referred to John as "Caleb" and tried to drive a wooden stake through him because she believed that he was the king of the vampires. John recovered and returned to work at the police station. A woman entered the police station and believed he was Caleb as well. The woman was Alison Barrington and after she left the station, she asked to meet with John on the pier. When John arrived, he found her son Rafe holding a dagger and kneeling over her lifeless body.
John took Rafe to the police station and Anna questioned Rafe about his mother's death. Rafe claimed that John had murdered his mother. Rafe's fingerprints were on the murder weapon, but so was a partial fingerprint that matched John's. Rafe and John each believed that the other was guilty until Rafe mentioned a ring that John had been wearing while he had killed Alison. John realized that there might be someone out there that looked similar to him that had committed the crime. While John investigated, the person that resembled him removed the dagger from the evidence room, took Rafe out of lock-up, and murdered police officer Bud Carlson. When John returned from his investigation, he was placed in police custody.
As John was held by the police, he realized that Lucy and Alison had believed that Sam was a woman named "Livvie Locke" and he feared that Sam and her son might be in danger while his doppelganger "Caleb" roamed free. John's fears were confirmed when he learned that Sam and her son were missing. He escaped from police custody with Rafe and Lucy and together they set out to save Sam and her child. John, Rafe, and Lucy learned that "Caleb" was actually a man named Stephen Clay. Stephen had escaped from a psychiatric facility and was accused of seven previous murders. They located Stephen at Spoon Island and rescued Sam and her son. John fought with Stephen and killed him.
All charges against John were dropped and he was reinstated at the police department. Sam remained grateful for all that John had done for her and they admitted their feelings for one another. They began to make love but pulled back when they realized that anything they would ever have together would be linked to the painful memories of their previous loves. John and Sam agreed to part ways as friends and wished that they had met when they were at a different place in their lives. After Sam left, Anna arrived and announced that John had to leave Port Charles. She explained that he had been called back to active duty by the FBI and was needed immediately in Quantico.