This season on Prison Break, Michael (Wentworth Miller) and Lincoln (Dominic Purcell) have been on the search for Scylla, the one all encompassing Company document that they can use to secure their freedom. Lincoln got caught up trying to make a deal with the Company and ended up working for them. Michael and Sara (Sarah Wayne Callies) struck out on their own pitting brother against brother. Michael and Lincoln’s mother, Christina comes into the picture but later reveals that Michael and Lincoln aren’t related – Michael is her only son. Christina sets up a plan to assassinate the Prime Minister of India’s son and blame Lincoln and the Chinese for the murder. Now that tensions between India and China are running high, Christina planned to play the two countries off of one another to get the highest price for Scylla and all it’s military technology. Unfortunately for her, Michael and Lincoln steal the Scylla briefcase from her just before her plan was completely. Michael runs away with the case, the General and T-Bag (Robert Knepper) capture Sara while Christina captures Lincoln and both parties want Michael to turn over the briefcase. Who will he choose? The Love of his Life or Lincoln, his supposed brother and the man he’s spent the last couple of years trying to save?
Michael tells Mahone that he’s going to save them both. Mahone tells Michael to save them one at a time because Sara doesn’t have a bullet in her chest like Lincoln does.
Lincoln tells Christina that Michael will never give it to her. Christina tells him to never underestimate how much Michael cares for him. Michael calls her up and tells her to meet him at the docks in 45 minutes.
The General taunts Sara with the question that probably haunts her daily: What if she had just left the infirmary door locked years ago? Sara also doesn’t think Michael will return Scylla. The General tells her that Michael’s heart will get the best of him. When Sara says she wishes Michael had killed the General that night, he asks T-Bag to get her out of his sight. T-Bag pulls out his pocket and asks Sara to take it. When she refuses, he says, “Either take my pocket or I take yours. Understand?”
Michael comes back to his base of operations with homemade explosives. Mahone tells Michael to give Christina what she wants. He thinks they can make a deal with her. Michael refuses.
Self wakes up in the emergency room. Agent Chris Franco and Wilson Wright come in to ask Self where Lincoln and Michael are. Agent Self tries to keep up his story that he’s undercover. The agents start to torture him and so Self tells them he can find out where they are. Agent Self asks for an exemption in writing in exchange for the information.
Hybrid Escalade! Dang! Nice ride Mahone. Christina tells her associate to dump Lincoln off the dock when she has Scylla. Michael and Christina meet up on the dock. She asks for his forgiveness and understanding. Michael demands to see Lincoln. Once he sees Linc, he tries to lead her over a trip wire. She doesn’t follow but her associate does. The police show up right when the homemade bomb kills Christina’s man. Christina now knows Michael was trying to kill her. Or at least hurt her really badly.
C-Note tracks down Sucre and asks him if he knows where Michael and Lincoln are. Sucre tells him he refuses to help the Feds. C-Note asks Sucre to call Michael and Lincoln and let them decide for themselves. C-Note says that the guy that wants the brothers isn’t government. If they give up Michael and Lincoln, his guy will give them their freedom.
Christina tells Lincoln that Michael cares more about winning than he does for him. Then she lets it slip that Sara’s pregnant. The Prime Minister calls and asks why he hasn’t received the technology yet. Christina tells Lincoln that if Michael doesn’t call in fifteen minutes, he’s going to wish Michael had let him fry at Fox River.
The General calls Michael. Michael tells the General that he’s being careful because the cops are everywhere. The General gives him one hour. T-Bag tells Sara that Michael’s messing up every chance of freedom he ever had. She questions whether or not T-Bag will really be free when this is all over and he says that he’ll be better than free: he’ll be employed. Sara asks what job the General would trust T-Bag with. Really, the only thing he’s getting after all this is a slit throat and an unmarked grave. She tells him the only chance he has at a life is to get out of there. Sara tries to bargain and tell T-Bag that she’ll wipe his slate with Michael clean so that Michael will help him and his mother. T-Bag says that the slate will never be clean between him and Michael.
Michael calls Christina and she asks if the explosion was meant for her. He asks to speak to Lincoln. Lincoln tells Michael that there isn’t enough time. He tells Michael that Sara’s pregnant and that he needs to go to her. Lincoln wants to die knowing that he did something for Michael. When he hangs up, Mahone asks what the plan is and Michael says that he doesn’t know. All he knows is that he has 43 minutes to get Scylla to the General. Michael asks Alex what side he’s on and Mahone says he doesn’t have a choice. Michael tells him to leave and go protect his wife.
Christina tells Lincoln that he’s worthless to her. She knows she was a horrible mother. She takes off her shoe and stabs his wound with it. Christina tells Lincoln that his real mother was dumb as a doorknob. The Prime Minister calls Christina and tells her that he’s leaving. She blames Lincoln for costing her three-quarters of a billion dollars and is about to kill him when Mahone calls. Alex tells her Michael’s giving Scylla back to the General. He tells her he’ll get her Scylla if she protects his wife. He also asks that she keep Lincoln alive. So if he brings her Scylla, she’ll protect Mahone’s family and give over Lincoln. How much double-crossing can we do in a season? Mahone goes to buy an identical briefcase.
T-Bag gets frisky and Sara demands that he stops messing with her. The General demands to meet Michael at a location of his choosing. He asks to met Michael in an abandoned parking lot by the beach and Michael agrees. Michael asks how he can trust that the General will let them live and the General gives a vague answer. Michael hangs up and tells Mahone, who’s there with the fake briefcase, that he’s happy Mahone’s been there to “have his back.” He hands Michael a case and Michael asks about Pam. Mahone says he has things taken care of. When the General hangs up, he yells at T-Bag when he starts to untie Sara. He informs T-Bag and Sara that the only thing Michael is getting today is a slow death. He then gives T-Bag permission to do whatever he wants with Sara.
Mahone calls Christina and tells her that he’s on his way. Her associate comes in and informs Christina that Agent Self has been offered immunity in exchange for his help. Meanwhile, Self calls Michael. Agent Self tries to get Michael to give up his location and Michael hangs up on him. A doctor comes in, asks to check with his patient and then tries to kill Don Self.
Michael “hides” the briefcase behind a pillar. When the General’s men arrive, they grab and open the fake suitcase. Micheal, in the meantime is scaling the walls of the loft. The General knows something’s up and races back to home base. Sara tries to convince T-Bag to let her go. He tells her it’s about revenge now. She begs him but he just promises to return her in one piece. As T-Bag continues to taunt and ruff up Sara, the handle she’s handcuffed to loosens. She tells him that she knows he has erectile dysfunction. The handle finally comes undone and she tries to hit him. She fails. Just as he’s unbuttoning his pants, Michael hits him on the head, knocking him unconscious. He’s about to hit T-Bag again, but Sara asks him not to.
Meanwhile, Mahone meets with Christina and offers up Scylla. He asks for proof that Pam is safe. Christina says that she has a man in place to protect his wife when need be and he refuses to trust her. She tells him she’s not going to give him everything he wants before she’s sure she’ll get what she wants. So, he hands over Scylla. Michael and Sara arrive back at his base of operation and he pulls out Scylla, which means Mahone only has part of it. Christina demands to make sure it works first and locks up Mahone.
Michael explains that if his mother could read his every move, he had to put Mahone in the forefront because she cannot predict Mahone’s motives. Michael knew the General would never bring Sara to the meet so he had to do what he had to do. She asks how big the explosion will be and he tells her it’ll be big enough to end all this. Big enough that they can start something new, if that’s okay with her. She joyfully agrees.
When Christina and her man go to test Scylla and it doesn’t work, Christina instantly knows Michael’s behind it. Michael and Sara talk about what their lives will be like once everything is over. They’ll talk about movies, work, and nursery schools. He tells her that it’s going to be great. Sara points out that all they have to do is survive. Mahone calls Michael right then and informs him that the detonator didn’t go off. Christina grabs him and demands he get it to work. Mahone then beats up Christina and her man, sets off the detonator manually and then takes cover.
The General is less than happy with T-Bag and his failure. The General tells someone to “move on Panama.” He’s just about to kill T-Bag when Sara’s phone rings. It’s Sucre. He asks where Michael and Lincoln are but T-Bag tells him that Christina has captured them both. T-Bag then tells Sucre to meet him in an hour at a park on 72nd after Sucre informs him that he’s with someone that can help. The General threatens to shoot T-Bag again and T-Bag tells him that he just set up a meeting with someone who will certainly draw Michael out of hiding.
T-Bag meets up with Sucre and demands he gives up the name of the person offering to help the brothers or else he’ll kill him. Sucre is unimpressed and demands Sara’s phone. Sucre and C-Note nab the phone and T-Bag.
The agents come in to find Self, post-heart attack and the doctors trying to revive him. One of the agents reveals that Self was working with Mahone. They demand to know where Michael and Lincoln are.
Michael and Sara pick up Lincoln and Mahone. Michael looks upset that Christina might be dead. She’s not. Lincoln tells Sara that they can’t go to a hospital. Mahone, Sara, and Michael get back to the base of operations and Mahone asks Michael whom they should trust. Michael tells Mahone that they should destroy Scylla. Alex Mahone reluctantly agrees. Just then, Paul Kellerman calls Michael. Why does someone always call at the perfect moment? Paul explains that he was freed by the same company his father worked for. He tells Michael that there’s a UN attache that will be in Miami at 5pm to receive Scylla from Michael. When he asks Kellerman how he knows they can trust him, Kellerman tells him that he just has to trust the United Nations. Michael hides Scylla in a cabinet then they all leave to go get supplies for Sara to help Lincoln.
C-Note and Sucre interrogate T-Bag. They try to get the General’s location out of him. They even try to promise him immunity. The General’s associate tells him to retreat but the General refuses. Just then, Lincoln’s cell phone pings a tower and the Company runs off to find him.
Lincoln wonders whether or not they should trust Kellerman. If what he says is true, they’ll walk away from all of this free men. He then tells Michael that they’re not brothers and Michael says he doesn’t believe it. Meanwhile, Sara and Mahone go into the hospital to steal supplies. Unfortunately, it’s the same hospital the agents are at with Don. They recognize Alex when he creates a commotion to cover for Sara and they arrest him. Lincoln tells Michael that they have to go get him but Michael tells him that Alex can wait until they are all exonerated. Just then, the General’s men show up.
C-Note and Sucre resort to torturing T-bag. Lincoln, Michael and Sara are brought back to the loft. The General puts Sophia on the television. They are going to slit her throat if they don’t give up Scylla. C-Note and Sucre bust in at the most opportune time. They shoot the two guards and then hold the General hostage. Lincoln wants Michael to kill the General and Sara pleads for him not to. Sucre convinces Michael to leave the General just as the cops show up.
They all pile into the Escalade and Sucre decides to create a roadblock. He asks for them to wait for him but after her blocks the road, the cops catch up and he screams for Michael to leave. Michael takes off and Sucre gets arrested. When they get back to the base, Michael leaves Kellerman a message telling he he better come through for them. Christina and her men show up shooting.
Alex Mahone tries to tell the federal agents about the Company. They won’t listen to him. They just want the brothers. They start threatening Sucre the same way. Sucre refuses to call Michael and Lincoln. He gets hauled off and gives a knowing smile to Mahone.
Christina sees the open cabinet and grabs Scylla. Michael holds her at gunpoint. She tells him that she knows he can’t kill his own mother. She tells him to pull the trigger for Lincoln. He shoots but there’s nothing left in the chamber. She raises her gun and says, “You were born a Scofield but you’ll die a Burrows.” Sara comes up from behind and shoots Christina in the back. Her gun goes off and hits Michael in the shoulder. She tells him that she’s going to take Lincoln to the hospital and he says he’ll take Scylla to Kellerman.
With his gunshot wound, he walks to meet Kellerman but is surrounded by agents. But whose agents? He gets led into a conference room and Kellerman shows up. Michael lists off all the names of the people Kellerman promised to exhonerate: Lincoln, Mahone, Sara, and Sucre. Kellerman reaches out for Scylla and Michael gives it to him. They test it and find out a piece is missing. Michael asks how they are supposed to get exonerated in some random office building. Kellerman tells him that if he doesn’t have it, they have to start running for their lives. Michael says he doesn’t want to run anymore and hands over the final piece. Kellerman’s associate leaves with Scylla and Kellerman tells Michael that it’s over.
Meanwhile, the General unlocks himself from the handcuffs just as Federal agents arrive to arrest him. In the boardroom, everyone’s given their immunities. They are asked to sign the forms and then they can leave. Michael and Lincoln hug after signing. Sucre asks to keep the pen. Michael and Sara share a long hug. C-Note and Sucre share a long hug. The agents tell Mahone that Pam is safe. Sophia and LJ are safe as well. Kellerman asks if they should exonerate T-Bag. Michael and Lincoln go to meet Theodore. They tell him he’s going back to prison.
Michael and Sara walk on the beach. He tells her that he’ll be a hands-on dad. Like keeping her side of the bed warm when she goes to feed the baby in the middle of the night. They’re going to be living in Chicago. She looks at him and tells him that she’s happy. Just then, his nose starts bleeding. He wipes the blood away and tells her he loves her.
Four years later, Mahone mails a birthday card to Pam. He has a new wife or girlfriend. Lincoln and Sophia discuss LJ’s finals. Sucre says goodbye to his daughter. Self has gone brain-dead and is in a care facility. C-Note is working as a UPS employee. Kellerman is a congressman. His old partner’s wife spits in his face as he gets into a town car. The general is getting executed. T-bag is in prison still, running things in his own special way. Sara and her son, Michael Jr. go to visit Michael’s grave where Sucre, Mahone and Lincoln are waiting for them. Michael Jr. lays flowers on Michael’s headstone. Lincoln leaves an origami crane on top. Michael died November 4, 2005.