Sam Manning was conceived in 2005 through the rape of his father, Todd Manning, by deranged Margaret Cochran. The baby originally was believed to have died before birth, along with his mother, although that was later revealed to have been an elaborate hoax orchestrated by Dr. Spencer Truman to frame Todd for the murders. Spencer had delivered Margaret's baby, which she named Todd Manning Jr., and then had disposed of it in a black market adoption. Margaret died in a van wreck before she could reveal what had happened with the baby.

Todd hired private investigator Rex Balsom to find the baby, and Rex soon discovered that the baby was actually his own godson Tommy, who had been adopted by Marcie and Michael McBain. Rex kept the truth to himself, but Todd eventually learned of his son's whereabouts after Spencer was murdered. Todd was awarded custody of his son in October 2007, but Marcie went on the run with the baby to avoid giving him up. Authorities eventually tracked down Marcie in Paris, Texas, and Michael convinced her to hand over the baby. Todd's son was returned to him in January 2008, and Todd renamed him Sam Manning in honor of his deceased mentor and friend, Sam Rappaport.

In May 2008, Todd lost custody of Sam to his estranged wife Blair Cramer after he got into a car accident and failed to have Sam secured in a car seat. Blair loved Sam as if he was her own and he remained under her care at Blair's family home, La Boulaie.

In June 2011, Sam was at the pool at La Boulaie when he was approached by a man bearing Todd Manning's original face. When Starr heard Sam talking to someone, the man hid and Sam said he was talking to a homeless man. Sam explained that the man had a line on his face and traced his finger over his own face to illustrate what the line looked like. Starr was taken aback but decided Sam had an imaginary friend. Later, Sam saw the man with Todd's original face being held at gunpoint by a well-dressed man. When the well-dressed man pointed the gun at Sam, intending to silence a potential witness, the man with Todd's original face kicked the gun out of the other man's hand and they wrestled for the gun. The gun went off, killing the well-dressed man. The man with Todd's original face told Sam not to say anything about what had happened and he agreed, thanking the man for saving his life. After the well-dressed man was found on the property, Blair brought Sam to the police station so John could question him about his imaginary friend. Sam revealed that his friend was real and had killed the other man to save his life. Sam then identified his friend from a photo of Todd before his plastic surgery.

Sam was surprised by Spiderman on his 7th birthday. But it turned out that the man in the Spiderman costume was his friend from the pool. The man took Sam to his room at the Minute Man Motel, where the man explained that he needed Sam's help to fight Spiderman's arch nemesis, the Green Goblin. Sam stayed in the motel room alone while the man went out on a mission. When Sam heard someone screaming in the next room, he put on his own Spiderman costume and went to investigate. Sam walked in on Echo DiSavoy about to kill his Aunt Dorian, who was bound and gagged. Sam sprayed Echo DiSavoy with a web of foam, stopping her in his tracks. Sam angered his father by insisting that he wasn't kidnapped and was with his friend, but Todd knew that the person Sam was with was the man with Todd's original face.

Eventually, it was revealed that the man with Todd's original face was indeed Todd Manning, and the man who had been living as Todd for the past eight years was his twin brother Victor Lord Jr., who had been brainwashed into believing that he was Todd and then given plastic surgery so he could infiltrate Todd's family undetected. In August 2012, Victor Lord Jr. was found shot to death in his home. An angry Jack, who refused to believe that the man he called "Scarface" was actually his biological father, blurted out to Sam that their father was dead and Sam's friend had killed him. Todd eventually remembered shooting Victor and was charged with his murder, but he escaped conviction after convincing the court that he was insane at the time. A shunned Todd set up a new life in Port Charles, N.Y. Meanwhile, no one knew that Victor Lord Jr. actually was alive and was being held prisoner by Allison Perkins.