Connor Bishop arrived in Port Charles shortly after the murder of his wife, Mary Bishop. He was determined to avenge his wife's murder and the events leading up to it. Mary, deeply depressed, lived in a cabin in the woods mourning the loss of her husband whom she believed had been killed in battle while serving in the military. When Nikolas Cassadine suffered amnesia after a car accident, Mary nursed him back to health in her cabin, while telling him that he was her husband Connor. Once the truth was discovered, Mary had a psychotic breakdown and went on a murder spree at the Quartermaine mansion. Nik cornered her near the boathouse and shot her. While in the hospital recovering from the gunshot wound, she was given a lethal overdose of medication by Lorenzo Alcazar, Sage Alcazar's uncle.

Connor was intent on taking from Nik what he believed Nik had taken from him. He kidnapped Emily with the intention of killing her, but she convinced him that Mary would not have wanted her memory honored that way. Connor still held Nik responsible for Mary's breakdown and wanted him to pay. Having witnessed Nik pushing Helena over a cliff one night after she had tried to kill Emily, Connor blackmailed Nik who eventually went to the police and confessed to killing Helena.

Unfortunately, Emily still needed Connor. Convinced that Helena had actually survived the fall, Luke hatched a scheme. Connor would impersonate Nikolas to draw Helena out of hiding and with Skye, Liz, Lucky, Dillon and Georgie's help they would all capture her. Emily taught Connor how to act more like Nikolas in order for the plan to work, during which time Connor's feelings for Emily grew. When Connor tried touching or kissing Emily, she made it clear to him that she was deeply in love with her husband. When circumstances put them together in a small cabin deep in the woods hiding from Helena, Connor's behavior grew more erratic and aggressive. Connor forced himself on Emily, but she fought him off by hitting him over the head with a discarded champagne bottle and ran for the basement. She locked the door and tried to find an escape while Connor demanded she open up. Grabbing a screwdriver from a tool chest, Emily went up the cellar steps prepared to open the door and confront Connor, but was greeted with silence. Just as she prepared to open the door, Connor crashed through the padlocked door at the bottom of the steps. Startled, Emily fell to the bottom of the steps where Connor picked her up and began hitting her, then pushed her back to the ground before violently raping her.

After the rape, Emily plunged the screwdriver into his chest then raced up the stairs to search for a cell phone. When she could not find a phone, Emily is forced to go back downstairs to check Connor's body to see if he had picked up the phone before coming downstairs. To her shock, Connor was not lying at the bottom of the stairs. She ran to the front door, intent on fleeing by foot, but found Connor standing on the porch holding a gun. Emily wrestled the gun away from him and shot him before he could attack her again.