While in town in 2012, John McBain begins to bond with Sam McCall, the pregnant wife of mobster Jason Morgan, Sonny's enforcer. John agrees to help Sam arrange a DNA test on her baby, to determine who the real father is. When she finds out that Franco, her rapist and Jason's twin brother, is the father of her baby, it puts a strain on her marriage, and she leans on John. The night Sam gives birth, John delivers her son, but when he goes to get help, he is beaten up by Jason's hired thugs. He's upset when he finds out Sam's baby died. Meanwhile, Téa arrives in town, pregnant, and John finds out she also gives birth to a baby boy the same night as Sam.
While in Port Charles, John's relationship with Natalie begins to strain over his continued absence. After confronting Sonny about his sister Theresa's death, John finds out that Joe Scully Jr killed her to protect his business. Joe is arrested. Sam finds John drunk on the dock, they watch Fourth of July fireworks and then kiss. After catching themselves, Sam chalks it up to the alcohol intake. John confesses there is something between them but he can't put his finger on it. John resolves to return to his family in Llanview.
John returns home to find out Natalie and Liam have gone to the airport. John immediately calls Natalie and finds out she's on a plane with Liam, to London. Natalie stole John's passport to prevent him from following her. John finds a note in the trash from Todd. John realizes that Todd sent the photo of him and Sam kissing on the docks to Natalie. John heads to Port Charles where he proceeds to assault Todd. Todd has John arrested but later drops the charges. After finding out Natalie has issued a restraining order against him after returning to Llanview, he and Alexis Davis, Sam's mother, talk about the best course of action.
After John helps save the PC water supply is saved, he's approached by Jason, who suspects that Sam's son was switched at birth with Téa's son. Jason says Heather Webber was the one who switched the babies, but John suspects Todd was involved in the switch, because he was with Téa that night. John travels to Llanview and gets a DNA sample from Victor, Téa's son, and hands it over to Jason. The DNA results come back, and Jason tells John that the baby is not Sam's.
John and Sam end up alone at Alexis's house, and nearly take the next step, but Sam stops the interaction. John figures out Heather has kidnapped Téa's baby. Anna tells him Heather is holding the baby hostage on the roof of General Hospital. John, Anna, Todd, and Téa arrive at the hospital, where they find out Sam and Jason are on the roof with Heather. Téa tries to head to the roof, but John stops her. Anna calls to Heather, saying the police have surrounded the hospital, and telling her to surrender. Heather becomes unhinged, and jumps from the roof, but the baby is saved by Jason. John goes to the roof after and accompanies Sam, Jason, and the baby into the hospital, and when Téa comes and tries to take her "son" back, John stops her, and he & Todd explain that her son was switched at birth with Sam's, and he never made it. Téa doesn't believe him, but when John shows the DNA test, and shares that the baby who died had hemophilia, a condition in Téa's family, she finally accepts the truth. He consoles Téa afterwards and is intent on making Todd pay. Todd is arrested, but his lawyer gets him released on lack of evidence.
John goes over to tell Jason about Todd being released, and instead finds Sam and her son, Danny. Sam says she has decided to stay with Jason, which John accepts. Meanwhile, Jason is presumed dead in a shootout involving Joe, Bernie Abrahms, and Duke Lavery. Jason goes to the pier to help Bernie, who was shot by Scully. Jason shoots Joe in self-defense, but before he can help Bernie, he is shot by Duke and thrown into the harbor. Duke shoots Bernie again, but fails to kill a fleeing Joe. Jason's body is never found and Joe and Bernie die.
John later comes to Sam's place, and hears her express how she doesn't believe Jason is dead after a shootout with Scully and Duke. John agrees with her, and says that he's going to look for Jason's shooter.
John leaves to investigate, and returns to Port Charles soon after. He finds Sam, and tells her that Jerry Jacks had Joe Scully released from prison. Sam thinks Jerry is holding Jason, but John disagrees, saying whoever shot Jason and killed Bernie is someone much higher up with a bigger agenda. Sam tells John that Heather switched her paternity test, and Jason is Danny's biological father. Sam is upset that John doesn't share her belief that Jason is alive, and sends him away. John, though, realizes Sam is grieving and in denial about Jason being gone.
In January 2013, he returns to Port Charles to tell Sam about what he found in Switzerland, and reveals that Faison was the one who shot Jason, and pushed him into the harbor, watching him sink. He helps Sam realize that Jason is gone, and never coming back. Later, he helps Sam tell Monica Quartermaine, her mother-in-law, what happened to Jason.
Later, Lucy Coe sees John, and calls him "Caleb." She claims that he is the king of vampires, and is on a mission to kill him. Sam shows up, then, getting between Lucy and John, but Lucy calls her "Livvie," who is supposed to be in danger from Caleb. John and Sam think she's crazy, and leave. Lucy corners John, however, and stabs him with a wooden stake. Sam then takes him to the hospital, where she catches Todd trying to escape police custody. John recovers, and Lucy is sent to Ferncliff, as people believe she is delusional. Lucy's husband shows up and says he knows Lucy's story is not true about Caleb Morley, and the woman he was obsessed with, Livvie Locke. However, soon after, another woman named Alison Barrington shows up, and also calls John "Caleb." She mistakes Sam for "Livvie," and says she and her son are in danger from Caleb. John is surprised when he finds no record of Alison ever having a son, so Sam goes to Ferncliff to see if Lucy sent Alison to back up her story.
John gets a call from Alison, telling him to meet her at Pier 52. John shows up, and finds Alison's dead body instead. Her son, Rafe Kovich, Jr., is next to her with the murder weapon. John arrests him, and he's taken into custody. Sam comes back, and tells John that Lucy said that Caleb was actually Rafe's father, not Alison's husband, Rafe Kovich, Sr. John finds out that Rafe claimed he didn't kill Alison, but that John did.
John shows up at the police station while Dante and Anna are investigating Rafe's disappearance. John is shocked when he finds out that they have him on surveillance taking Rafe out of his cell and taking the murder weapon from the evidence room. Dante tells him that Rafe and "John" left with another officer named Bud Carlson, and they found his dead body at the pier, stabbed with the same weapon that killed Alison. A nurse named Sabrina Santiago identified John as the killer in officer Bud Carlson's murder. John insists that he's innocent, but due to the evidence, Anna is forced to arrest John and put him in lockup.
While John is in lockup, Sam comes by. Sam asks where he was when Rafe escaped from lockup. John says he was at Port Charles University, talking to a professor named Jay Mosser about the ring Rafe saw on the killer's finger. Sam heads to PCU to get John's alibi, while Alexis comes in to build John's case. Lucy is arrested again, and John insists on talking to her alone. Lucy still believes he's Caleb, but John insists he's not, though he does believe that Caleb exists, and is trying to get Lucy and John out of the picture to get what he wants. Lucy starts to believe that Caleb and John might be two different people. She shares that Caleb wants two things: Rafe and Livvie, who looks just like Sam.
John finds out that Professor Mosser was also killed, but Anna realizes it couldn't have been John, because he was in lockup at the time of death. Meanwhile, Todd is recaptured and brought to the police station. However, he claims that he saw John strangle Heather and throw her into the harbor at Pier 52, then try to kidnap Danny. Todd says he was trying to save Danny when Anna and Sam showed up, and took Danny back. When John hears this, he realizes it was Caleb because he was at the police station when this happened. Rafe is recaptured, as well, and brought to lockup.
While Todd, John, and Rafe are in police lockup, they compare their stories. Rafe starts to believe John when he says that Caleb exists, and is actually committing the crimes. Todd reveals that when Caleb was trying to strangle Heather, he said that he was going to use Danny to get to his mother. John realizes that Caleb thinks Sam is Livvie, and his target is actually Sam, not Danny. Before he can tell Anna, she comes and tells him that Sam & Danny are missing. John is desperate to get out, in order to save Sam & Danny. Sam's sister, Molly Lansing, comes in, trying to break Rafe out on Lucy's orders. John realizes what she's doing, and convinces Molly to let him out too so he can find Sam and Danny. Lucy causes the fire alarm to set off, and Molly is able to let John and Rafe out of their cells, while Lucy escapes from the distracted officers.
John, Lucy, and Rafe go to PCU and find information about Caleb Morley. His real name is Stephen Clay, and he used to be a rock singer who went insane after the death of his wife, Livvie Locke Clay. He started to believe he was an actual vampire, and went on a killing rampage, killing seven people. Stephen was locked up, but escaped from the sanitarium in 2011. He's fixated on finding his dead wife again. Livvie is a dead ringer for Sam, and John realizes Stephen believes Sam is Livvie, which is why he kidnapped her. Lucy mentions a dream she had about "Caleb," and John deduces that Stephen has taken Sam & Danny to Wyndemere.
The three head to Wyndemere, where they find Danny alone, but safe. They realize both Stephen Clay and Sam were there not long before, and John realizes they went into the tunnels. John and Lucy head to the tunnels, while Rafe watches Danny. John finds Stephen and Sam, who has a bite mark on her neck. John tries to stop Stephen, only to be overpowered and tied up. Lucy then shows up and tries to kill him, but she's also overpowered. However, she's able to distract Stephen long enough for John to get free. He kills Stephen when Sam distracts him by calling Stephen "Caleb." Caleb is thought to be dead, but his ring lights up signalling a possibility that he could come back. That never happened in the years following.
John, Lucy, and Rafe are taken back to PCPD and held in the interrogation room while Mayor Lomax, Anna, and District Attorney Martinez discuss their course of action. Sam shows up and tells the press that the three prisoners saved her life and Danny's. Eventually, the mayor "spins" the story, saying that John, Lucy, and Rafe were working in tandem with Anna to apprehend Stephen Clay. John is released, and resumes his job at the PCPD. Rafe comes to the hotel and says that he was involved in a fight. John wanted Rafe to stay with him, but Social Services doesn't allow it. John and Sam make out, but before it goes further, Sam wisely stops it. On March 20, John learns that the FBI has an assignment and that he must leave Port Charles for a while.