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John and Natalie accept the offer of a double wedding. On the day of the wedding, Clint's employee,
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Vimal, stops the wedding and reveals the paternity switch he did on Jessica's child, and the fact
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Natalie also had a paternity test done. Natalie then tells John the paternity test for Liam says
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Brody is the father, and John leaves her, devastated. John initially sleeps with Kelly Cramer (Gina
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Tognoni) to hurt Natalie, but continues to do so for months. John is shown to be conflicted with
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his love for Natalie, but being hurt by her betrayal and his love for Liam but not being able to
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accept he was not the father. Marty is released from the institution, and is intent on getting John
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back.
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Marty soon reveals to her psychiatrist she switched Natalie's paternity test. John is Liam's
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biological father. When Natalie finds out, she tries to tell John, only to be thrown off the roof
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by Marty. Marty also stabs Kelly, and escapes with Liam. Eventually, Marty leaves town, and Liam is
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found, and returned to Natalie and Brody. John and Natalie have a conversation about his inability
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to 'get past' Liam being Brody's even though he wants to. Natalie, believing John can never forgive
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her, decides to move on with Brody. John realizes he's still in love with Natalie, and breaks up
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with Kelly. When he goes to tell her, though, he finds out Brody proposed to Natalie, and she
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accepted. John decides to leave town and heads to Seattle to be with his brother's family. However,
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at the airport, Natalie shows up and tells John about him being Liam's father, and how Marty had
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switched the results. Natalie also found out Brody knew, and kept it a secret. Natalie and John go
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back to her house to be with Liam, only to find him gone. They realized Brody had taken Liam. They
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tracked Brody down to his family home, and he eventually handed Liam back. Natalie and John tried
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to talk about their relationship, but kept putting it off. After Natalie is kidnapped by Mitch,
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John saves her, and they reconcile.
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"Todd Manning" is actually revealed to be Victor Lord, Jr., Todd's twin brother who had taken his
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place for eight years. Victor is found dead soon after, and John helps Téa try to find his killer.
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Initially, evidence points to Tomás Delgado (Ted King), Téa's brother, but both John and Téa figure
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out the real Todd Manning (Roger Howarth), recently returned, framed Tomás to cover up his crime.
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John arrests Todd in the finale.
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2012–13
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When One Life to Live ended January 13, 2012, John was happily reunited with Natalie, and planning
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on raising their son together. However, commercials aired that John would be heading to Port
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Charles General Hospital for a crossover event with Starr Manning, Todd Manning and Blair Manning.
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It was not clear how his relationship with Natalie and his son would be resolved as they were not
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announced to be a part of the initial crossover. Viewers soon find out when John arrives in Port
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Charles, he is still in a relationship with Natalie.
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John McBain arrives in Port Charles after Blair calls him to inform him Todd has jumped bail to
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come there. John comes to the courthouse, where Todd is holding a gun on Sonny Corinthos (Maurice
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Benard), threatening to kill him because he believes Sonny is responsible for the car crash that
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killed his granddaughter Hope and her father Cole. John arrests Todd and takes him back to Llanview
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to stand trial for the murder of Victor. He is released, and comes back to Port Charles when Starr
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is arrested for trying to kill Sonny. John decides to return to Port Charles to take down Sonny,
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whom he blames for his half-sister Theresa's death years before. John's half sister was a new
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character created by Ron Carlivati to help facilitate the crossover. The explanation given to the
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audience why Teresa was never mentioned by Eve, Michael or Shannon McBain on One Life to Live was,
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John and Thomas McBain were the only family members which knew of her existence. Thomas McBain was
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shown on One Life to Live as a ghost and in recreations of John's history, but he did not mention
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Teresa on the show. John goes to see Anna Devane (Finola Hughes), whom John knew while he was with
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the FBI, and she is able to pull some strings to get him FBI clearance of 40 days to investigate
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Sonny. John makes it clear to Sonny he wants to take him down because he killed his sister, and
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Sonny maintains he is not responsible for her death. Sonny blames Joe Scully Jr. (Richard
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Steinmetz), and is proven to be true. During John's conversations with Anna, Anna warns him his
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need for revenge could cost him his family.
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During this time, John meets Sam Morgan (Kelly Monaco), the pregnant wife of Sonny's enforcer Jason
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Morgan (Steve Burton). Sam confides in John about her problems with Jason and her pregnancy and
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that she was raped by Franco (James Franco). John uses his experience with the paternity debacle he
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went through with Natalie as a common ground they can relate. After Sam finds out Jason and Franco
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were twin brothers, John is able to get Sam a DNA sample of Franco from the FBI so she can have a
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paternity test done on her baby. After it is revealed the baby is Franco's and not Jason's, Jason
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cannot accept the baby and Sam moves out, at which point she leans on John for support even more.
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Jason doesn't like Sam spending time with John and is worried he is using her to take him and Sonny
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down.
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John helps Sam give birth to her son, and tries to get help but is prevented by Jason's hired
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thugs. On the day Sam's baby (Danny Morgan) is born, Todd Manning and Heather Webber switch Sam's
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live baby with Téa Delgado's stillborn son, Victor Lord III. Téa tells John that Todd saved her
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son's life, and she takes the child home to Llanview, Pennsylvania. On a night when John is
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depressed about the role he might have played in his sister's death, and Sam is sad about the
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passing of her baby, John and Sam kiss, but decide they cannot go further. Todd, upset with John
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about the role Todd believes John played in the destruction of Todd and Blair, mails Natalie a
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photo of John and Sam kiss at the harbor. John, who had been back to living in Llanview, returns
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home with dinner to discover Natalie and Liam gone. Clint's driver arrives and delivers a note in
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Natalie's apparent handwriting telling him she hopes it was worth it referring to his cheating on
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her. John calls Natalie, and she tells him she's in london. Although John is prepared to follow
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her so that he can grovel for her forgiveness, he discovers she took his passport with her. John,
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upset his life is falling apart, returns to Port Charles to confront Todd for destroying his family
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by sending Natalie the picture. John receives a restraining order from Buchanan enterprises, where
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Natalie's father owns, supposedly filed by Natalie. Unable to stay in Llanview, John stays in Port
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Charles and enlists Alexis Davis (Nancy Lee Grahn), Sam's mother, to help him see his son again.
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John hopes once the restraining order is lifted, he and Natalie can reconcile. John gives up on
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that aspiration, when he gets a letter in Natalie's handwriting from Buchanan Enterprises telling
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him, she has moved on and is in love with someone else. Meanwhile, Jason approaches John with the
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suspicion Sam's child is alive, and was switched with Téa's baby. They get the proof, and John
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helps Sam and Jason reunite with the baby, and also helps Téa realize the truth about her son being
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stillborn.
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Jason is shot the night Sam reunites with him, and presumed dead. John tries to help Sam deal with
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her denial over Jason being dead. Sam tells John that Heather tampered with the paternity test.
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Jason is her son's biological father. In November, John has been in Port Charles for a few months
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unemployed, waiting for Alexis to resolve his visitation. Alexis explains to John, his chances of
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getting to see his son again would improve if he can show he can provide for the child. As a
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result, John asks Anna, now Commissioner of PCPD, for a job. She hires him as Detective Dante
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Falconeri's (Dominic Zamprogna) partner. Together, with the help of Anna's ex, Robert Scorpio
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(Tristan Rogers), they capture Cesar Faison (Anders Hove), a wanted criminal who shares a history
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with Anna. John reveals to Sam that Faison was the one who shot Jason, helping her realize Jason is
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dead. The restraining order is later revealed to have been filed by Natalie's father, Clint
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Buchanan, without her knowledge. Clint felt John was not a worthy partner for his daughter, or
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father to his grandson, after he cheated on Natalie, while she was taking care of their son.
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Once, when John is watching Danny, Sam's son, Lucy Coe (Lynn Herring) sees him, and calls him
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"Caleb," the king of vampires. Sam comes back, and Lucy calls her "Livvie." Lucy stabs John, and
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Sam takes him to the hospital. Lucy is declared insane, but later a woman named Alison Barrington
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(Erin Hershey Presley) shows up, and also calls John "Caleb." Soon after, Alison is found dead, and
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her son, Rafe Kovich, Jr. (Jimmy Deshler), becomes the primary suspect. At the station, however,
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Rafe points the finger at John as the killer, and there proves to be evidence to back it up. John