Sam, Lulu and Carly are taken by the crazed artist Franco. Jason finds Carly in Franco's workshop and saves her. Later, Franco confesses where he is holding Sam and Lulu Spencer. During this time, Sonny is put on trial for Claudia's murder. The cover-up is blown when Dante discovers the truth and tells the court what really happened. Judge Carroll, furious that the trial was a farce, makes an example of Michael by giving him the particularly harsh sentence of two-to-five years in the Pentonville Adult Correctional Facility. To protect Michael, Jason makes a deal with Claire and is sent to Pentonville as well. Dante, Claire, and Jax convince the judge to release Michael on parole. Jason is forced to remain in Pentonville. Franco returns to Port Charles to resume his feud with Jason. Jason makes a deal with Dante and Claire and is temporarily released from Pentonville to draw Franco out of hiding. Jason and Dante go to L.A. to find Franco. They thought Franco died (from his fall off the roof), but it was someone else. Jason is permanently released from Pentonville on a technicality after Claire discovers a loophole in his plea bargain. Jason later goes to Rome to serve as a bodyguard to protect Brenda from the Balkan. In early 2011, Sam finds out about a fertility reconstruction surgery that might give her the possibility of having a baby, and she decides to have the surgery. Jason and Sam discover that Brenda's defense attorney, Theo Hoffman, is the Balkan, and go to stop him. Brenda is seemingly killed in a car bomb after her wedding to Sonny. Everybody is shocked to discover Sam within the limo, with no sign of Brenda. Due to bomb-proofing, Sam survives the explosion with only a concussion and temporary hearing loss. Jason, Sonny, and Dante track down Brenda, finding her near death after being injected with a neurotoxin.
On March 18, 2011, Jason's son, Jake gets hit by a car. Jake is rushed to the hospital, and Patrick and Robin Drake operate on him, but Jake dies on the operating table. His kidneys are donated to save the life of Carly's daughter Josslyn. When Abby's ex, Brandon, is killed, he and Michael are suspects. Jason figures out that Anthony Zacchara had Brandon killed to try to lure Michael into the business. Jason runs interference while dealing with Luke, who is revealed to be the hit-and-run driver who killed Jake and wants Jason to kill him. Jason realizes that he never wants to part with Sam and proposes to her, and she accepts. Carly comes by when Jason and Sam are planning their wedding, asking for Jason's help to stop Jax from taking Josslyn. On their way to Carly's house, Jason and Carly get into an accident with Elizabeth and Lucky's wife, Siobhan. Jason is rushed to the hospital and has to undergo surgery. Patrick performs a risky operation that nearly kills Jason, but is successful. Jason recovers and comes home in time for the wedding. Monica gives Alan's wedding ring and Edward gives Lila's wedding ring to Sam and Jason. Sam and Jason marry in a garden of a Chinese restaurant in the Asian Quarter. The two go on a romantic honeymoon in Hawaii but are interrupted by Carly and Shawn telling them that Franco is back. On their last night, Sam and Jason are drugged by Franco. He locks Jason in a room and forces him to watch as he apparently rapes Sam. They return to Port Charles and Jason begins losing his temper and searching for Franco. Jason is tormented by visions of what he saw on the TV and the guilt of not being able to protect his wife. Jason eventually kills Franco but when he returns home, Sam tells him she's pregnant. They have a paternity test done and Dr. Kelly Lee confirms to Jason that the baby Sam is carrying is Jason's child.
Robin informs Jason that his outbursts are caused by cerebral edema as a result of the surgery. He later discovers that his condition is inoperable. Robin develops a medication to save Jason's life but dies in a lab explosion caused by a gas leak. Patrick furiously blames Jason for her death and resolves to let him die. However, after a talk with Robin's mother, Patrick changes his mind and decides to honor Robin's final request: save Jason's life. When Jason starts to recover, he and Sam decide to figure out what the DVD meant that Franco left. The search takes Sam to Ferncliff, where she meets with Heather Webber, who tells Sam that Franco is Jason's fraternal twin brother. Sam runs another DNA test and is devastated when it says Franco is the father. She tells Jason and he has a hard time accepting the news. Jason and Sam separate to work on their marital issues. When Jason realizes that he can love and accept the baby as his own, he goes to the motel where Sam is staying to tell her, unaware that she has given birth to a boy that she names Jason Morgan Jr. A torrential rainstorm prevented Sam from getting to the hospital and she gave birth in the motel with the help of John McBain. Jason is jealous of Sam's friendship with John so he sends two guys to beat John and convince him to go back home. This action prevents John from getting Sam and the baby to the hospital. Sam leaves the motel with the baby to look for help and after placing the baby somewhere safe she passes out. Jason finds Sam and a dead baby and is forced to tell her that her child has died. They are unaware, however, that Todd Manning and Heather switched Sam's son with the late newborn son of Téa Delgado. It is later discovered that Heather switched the paternity results and made it appear that Franco is the father of Sam's child when in reality, the baby is Jason's biological son, but this truth remains unknown to everyone except Heather Webber, Johnny Zacchara and Todd Manning. Jason tries to comfort Sam over her loss and make things right between them.
Sam pushes Jason away in her grief and kisses John McBain. Meanwhile, Jason confides to Elizabeth everything that has happened, and runs into her after seeing Sam and John kiss. He contends that his marriage is over and kisses Elizabeth impulsively, but immediately regrets it. The next day, Jason takes his ring off, and gets yelled at by Elizabeth's brother, Steve, for kissing Elizabeth, which Sam happens to hear. Jason then confronts her with the fact that she kissed John, and Sam leaves, saying that Elizabeth is welcome to Jason. Jason and Sam agree to divorce and share a tearful goodbye. He finds out that Alexis and Josslyn have a mysterious illness after disappearing. He teams up with John to investigate and finds Dr. Ewen Keenan at Wyndemere, making him suspicious. Eventually, the culprit is found to be Jerry Jacks, who has poisoned the water supply of Port Charles and will only fix it in exchange for a ransom. Jason goes after Jerry with Jax, who has recently returned, and John. Eventually, he finds out that Ewen is also a part of the scheme. When Ewen abducts Elizabeth, Jason goes after them. He shoots and kills Ewen and gets shot in the leg himself. When they get to the hospital, Sam and John come in after she fell unconscious, and John worries Sam has been infected.
When Patrick comes in to treat Sam, he also gives Jason and Sam information about Sam's baby, saying there was no way the doctors could have saved him, even if he was brought to the hospital, because his lungs weren't developed. Sam and Jason come to terms with the loss, and decide to move on, despite the love that's still between them. Jason looks at the baby's file, and finds a discrepancy: Sam and Franco's blood type is different from the baby's. Jason asks Spinelli to run a second test, which confirms his suspicions: the baby that died wasn't Sam's . He and Spinelli deduce that Heather was involved, and would have switched Sam's baby with another. When Jason talks to Steve about this, Steve mentions that he treated Téa Delgado and her son the night of the storm. When the blood type matches Sam's and Steve confirms that Téa's baby had a blood disorder Sam was diagnosed with, Jason is positive Téa's baby is Sam's. Jason calls John to share his suspicions, and John figures out Todd was involved in the switch. He asks John to get a DNA sample from baby Victor, Téa's son, to confirm his suspicions. Meanwhile, Jason shares his findings with Elizabeth. When the DNA results come back, Jason is disappointed to find out that it's not a match. However, Elizabeth later confesses to Jason that she switched the DNA test and gave him the wrong results. She admitted that Téa's baby is Sam's. When she leaves, Jason calls John, and shows the DNA results. Jason goes to tell Sam, and John leaves to tell Téa. However, Jason is not able to tell Sam, because Kristina comes in with Trey Mitchell, her husband, after nearly being killed by Joe Scully, Jr., Trey's father and Sonny's nemesis. When they leave to tell the police, Jason gets a call from John saying the baby has been kidnapped by Heather.
Jason talks to Steve and lets him know that Téa's baby is Sam's, and that his mother has kidnapped him. Jason doesn't want to tell Sam the truth until they find the baby, but Steve convinces him to. Jason agrees, and goes over and tells Sam that her baby is alive and Heather has kidnapped him. They head over to the hospital after John comes by. They talk to Steve, who was attacked by Heather when she came to his house, and learn that she thinks the baby is her second chance at motherhood, and has no intention of giving it up. Jason and Sam wait at the hospital while Dante, John, and Anna Devane track down a lead. Jason asks Dante for a copy of the PCPD pictures they have of the baby and shows them to Sam, who is overjoyed her son is healthy. She expresses concern about Téa, who is going to hear that her son died once they find Heather.
Heather ends up in the hospital when Jason Jr. runs out of his medication. She runs into Olivia, who is hurt and found by Jason and Sam. They follow Heather, cornering her on the roof. Eventually, Heather is trapped when the police arrive and surround the building. Heather becomes unhinged and jumps off the roof. However, Jason saves the baby while Heather hits the ground. He puts Sam's baby back in her arms. Sam is overjoyed to be holding him, and Jason is glad he's finally seeing Sam happy. On October 22, 2012, Jason is called by his accountant Bernie to Pier 52 to handle a situation, unaware that he has interfered with plans made by Cesar Faison (who had been posing as Duke Lavery). He shoots Joe Jr., who is about to finish off Bernie, but is later shot by Faison and attempts to fight for his life. When Jason suddenly stops moving, Faison kicks him down in the water, and he is presumed dead. Not long after he disappears, Sam finds out Jason is Danny's biological father.
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