Michael and Sara talk about the ordinary life they're going to lead when this is all over. Mahone calls and says that the bomb meant to take out Christina didn't go off. Michael tells him he'll have to trigger it manually. Christina enters and demands to know why they can't access Scylla. Mahone pretends ignorance. Christina orders Downey to kill him just as Mahone finds the manual switch on the bomb. The beeping of the bomb distracts Downey just long enough for Mahone to overpower him and escape with Linc. Moments later, there is a tremendous blast that knocks Downey and Christina down. Outside, Michael's just arrived with Sara. Sara wants to get Linc to a hospital, but Linc says that'd mean jail. Michael regards a big hole in the building where Christina was, but we see inside that Downey's body shielded Christina from the blast. Her finger begins to twitch.
At the loft, Krantz is about to kill T-Bag for his many failures when a phone rings. It's Sara's; she accidentally left it behind. T-Bag is allowed to answer the phone and finds Sucre on the other end. Sucre asks where Michael and Lincoln are; T-Bag says their mother has them. He's got an idea of where, but he's scared to talk on the phone. They arrange a meeting in the park in an hour. Krantz reluctantly sends T-Bag out with an operative. T-Bag meets with Sucre and points out the operative to him, telling him he's walked into a trap. Sucre, smirking, demands Sara's phone. T-Bag looks up again and sees that the operative is dead. A moment later, C-Note shows himself. They take T-Bag hostage. C-Note reports back to his mysterious employer that he's got Sara's phone; there are a lot of calls to one number. It must be Michael.
Michael decides the best thing to do is destroy Scylla; Krantz will have them killed no matter what they do. Suddenly, Michael's phone rings, and on the other end... is Kellerman. Not dead after all, he was freed by a group trying to bring down the Company, the group founded by Michael's father. He tells Michael to get Scylla to a U.N. attach? at 5pm at the footbridge in Declan Plaza. Michael tells him to stop Krantz from pursuing their families. Kellerman agrees, and says when Scylla is delivered, all their slates will be wiped clean. Michael doesn't know whether to believe him. Kellerman says that Scylla can change the world for the better; he doesn't need to trust Kellerman, he just needs to trust the U.N. Sara says that Linc's out of time; she needs a needle, syringe and chest tube right now. At the loft, Krantz and Ralph realize T-Bag is either captured or dead. They get a ping off of Linc's cell phone; Ralph and another operative head to the location. Elsewhere, Sucre and C-Note interrogate T-Bag. They want Krantz's location. T-Bag won't talk. They string T-Bag upside-down and tell him his eyeballs will burst. He's still not talking, still clinging to the idea of becoming a respected "gentleman" in the Company's employ, but the treatment is getting to him.
At the hospital, the FBI agents interrogating Self check his files and see that Mahone's involved. Self's nearly comatose and his brain is quickly wasting away, but he can move his hand and write... but the only message he'll write is "F.U." Meanwhile, Sara arrives at the hospital with Mahone in tow. She grabs a doctor's lab coat and slips into a supply closet. When a nurse is about to go in, Mahone distracts her by asking questions... and attracts the attention of the one of the FBI agents. In the car, Linc tells Michael if he has to leave him, he should. Michael says not a chance, they're brothers. Linc says that's not what Christina said. Michael says she was just messing with their minds... and even if it's true, it doesn't change anything. Sara emerges from the supply closet to find Mahone being arrested. He nods to her to leave and she hightails it back to the car. Sara gives Linc an injection that will only last for a while. Michael says they have to leave Mahone, but once they deliver Scylla to Kellerman, it'll buy Mahone his immunity. Suddenly, the passenger window explodes and shatters, shot by a Company operative. At the driver-side window is Ralph, who takes them all back to Krantz. Michael claims not to have Scylla. Krantz turns on a TV which shows a live feed of Sofia being held at gunpoint and demands Scylla again. Meanwhile, Mahone is interrogated. He insists that he and the others have been set up, but the FBI aren't listening. They just want the location of Michael and Linc. At the loft, the stalemate is broken by the arrival of Sucre and C-Note; T-Bag must have finally talked. They shoot Ralph and hold Krantz at gunpoint before he even knows what's happening. Michael orders Krantz to have Sofia released, and he does so. Michael's about to kill Krantz. Linc eggs him on, but Sara and Sucre talk him out of it. Krantz is cuffed to the banister and left behind. Michael asks C-Note why he trusts Kellerman; C-Note admits that Kellerman's the only option they've got. As they bundle into the car, police sirens wail. They're nearly trapped, until Sucre uses his own car to cut the police off. He is arrested as Michael, Sara, Linc and C-Note get away.
Christina and her men track Michael down via his cell phone. She shoots C-Note in the legs and nearly walks off with Scylla, but pulls a gun on her. He hesitates to pull the trigger for a moment, but Christina goads him and he fires... but the gun just clicks. Jammed. Christina prepares to shoot him, telling him he was born a Scofield but will die a Burrows. Suddenly, two shots ring out; Sara has shot Christina dead at the moment she fired at Michael. Her shot went wild and struck Michael in the shoulder. Sara takes Linc and C-Note to the hospital while Michael delivers Scylla to Kellerman. As Sucre stays as tight-lipped under FBI interrogation as Mahone was, Michael goes to the rendezvous point... where he is taken hostage at gunpoint. However, it transpires that these are Kellerman's men. He just wanted to make sure Michael wasn't followed. In an office building, Kellerman tries to boot up Scylla for Solomon Okella, the man from the U.N., but it doesn't work. Michael's withholding a piece. He wants proof that the Okella's legitimate. Okella's ready to walk away. Tired and beaten, Michael says he doesn't want to run anymore. He gives up the missing piece, and Scylla boots up. Okella's satisfied. So's Kellerman, who says it's over - Michael did it.
Krantz finally frees himself from the handcuffs, only to be arrested by a team of cops who have just arrived. Not long after, Michael, a healthy Linc who's gotten the treatment he needs, Mahone, Sucre, Sara and C-Note are seated around a table with Kellerman, who presents them all with statements to sign. They all sign and are free at last, and Kellerman confirms that all their loved onces are safe as well, but there's one final piece of business to take care of. T-Bag wants exoneration for his help. Kellerman leaves it up to them. Michael and Linc approach T-Bag, who is being held in the hallway. He begs for mercy and forgiveness. Linc says they took a vote and he's in luck... T-Bag gets a stick of gum for the ride back to prison.
Later, a jubilant Michael and Sara walk along the beach. Michael says he's going to be a hands-on dad. They're both happy. Suddenly, Sara stops short. Michael has a nosebleed. They both pale, knowing what this could mean. Michael insists he's fine. They hold each other tightly.
Four years later. Mahone mails a birthday card to Pam, then kisses and walks off hand in hand with Felicia Lang. In Chicago, a happy Sucre is playing with his little girl and tells her he'll be back in two days, while C-Note, working for UPS, luxuriates in his freedom and normal life. In Central America, Linc and Sofia live happily together. LJ's in school. They hug goodbye and Sofia tells him to get home safe. In a convalescent home in Chicago, a brain-dead Don Self stares out the window and drools. On death row, General Krantz is led to the electric chair. In Washington, Kellerman is now a crusading Congressman, well-loved by the press... but not by Danny Hale's widow, who arrives to spit in his face in front of the press photographers. And in Fox River, T-Bag hears an inmate talk about "the captivity of negativity." He's reading a book about GATE. Saddened at the reminder of the white-collar life he nearly had, he tells the inmate firmly that he never wants to see that book again. The inmates fear him; he's a leader among prisoners once again... and a young boy in his entourage is holding his pocket. And at a street fair in Central America, we see that Sara has a small, pendant-shaped scar on her shoulder in the shape of a snake. She calls to Michael that it's time to go... but the Michael she's speaking to is a child. Her child, Michael Jr. She says it's time to go see Daddy. They arrive at a cemetery, where they meet up with Linc, Sucre and Mahone. Michael Jr. puts flowers on a headstone... while Linc leaves an origami crane. Everyone pays their respects. As they leave, we see the inscription on the headstone:
Michael J. Scofield
September 8, 1974 - November 4, 2005
Husband, Father, Brother, Uncle, Friend
"Be the change you want to see in the world."