According to Michael's plan, Mahone hands a fake Scylla to Christina. It's booby-trapped but ends up in the hands of FBI Agent, Chris Franco. Bagwell meets Sucre and C-note, but is caught while they hope that an offer of help is real. The General catches the brothers and raises the stakes with more kidnapped relatives. Michael manages to escape with Scylla. The gang must decide whether to believe an offer from Paul Kellerman, and hand it to UN representatives in exchange for full pardons.
The identity of the mysterious Paul is revealed and the Company falls with Christina dead and General Krantz sent to the electric chair. Michael, Lincoln, Sara, Mahone, Sucre, C-Note and Self have their records clear and rebuild their lives.
After the general catches the brothers and raises the stakes by abducting more of their relatives, Michael escapes with Scylla.
- Michael and Sara discuss their future in the car. Mahone calls to say faux Scylla hasn't exploded. Michael tells him he must detonate it manually. Christina shows Mahone that Scylla appears to be wiped clean. Sitting at the computer Mahone manages to trigger the explosion. He knocks Christina and Downey aside and runs into the room with Lincoln just as the device blows up.
The General is furious at T-Bag for allowing Sara to escape. Just before the General shoots T-Bag, Sucre calls Sara's phone. T-Bag answers it and pretends to still be working with Michael. Sucre tells him about the mysterious Paul character and they set up a meeting.
Michael and Sara pick up Mahone and Lincoln. We cut to the office and see that Christina has survived the explosion.
During the meeting T-Bag demands Sucre give up the identity of Paul. C-Note and Sucre get the jump on T-Bag and his Company guard. Sucre calls Paul and says they have Sara's phone.
A doctor tells Franco that Self may have bleeding in his brain or suffered a heart attack. Wright shows Franco a mug shot of Mahone who they know now had been working with Self and the brothers. When it appears Self responds to Franco's voice by moving a finger, the agent demands the doctors hold off on his CT scan.
Michael & Co. agree to destroy Scylla. Michael's phone rings with Paul Kellerman on the line. Kellerman has been working with the anti-Company group started by Michael's father. A United Nations attache will be in town to get Scylla from Michael. The phone dies and Lincoln begins vomiting blood.
Sucre and C-Note question T-Bag about the Generals whereabouts. They offer immunity list if he helps the UN. C-Note starts roughing him up.
Becker and the General receive word that Lincoln's phone was tracked to a downtown location.
Lincoln tells Michael he doesn't trusts Kellerman. They discuss the fact they are not biological brothers with Michael saying it doesn't change anything.
With Self refusing to help Franco, the agent walks into the hall. Mahone and Sara have snuck into the hospital to grab medical supplies for Lincoln. Sara leaves the hospital as Mahone is being placed in handcuffs. While Sara works on Lincoln in the back seat Becker knocks on the driver's side window with his gun.
Sucre and C-Note hang T-Bag upside in an attempt to get him to talk. He begins to scream.
Michael, Lincoln and Sara are brought to the General's loft. When Michael tells him they don't have Scylla the General turns on a monitor and shows them he has Sofia in custody. If Michael doesn't hand over Scylla the General will force Lincoln to watch as his girlfriend's throat is slit.
Franco and Wright question Mahone. He tells them Lincoln and Michael are innocent and tells them about The Company. Franco seems focused on Michael and Lincoln.
Michael and The General negotiate for Sofia and Sara. C-Note and Sucre sneak in through the deck and shoot Becker and another guard. Michael has the General release Sofia and is ready to kill him. Sara tells Michael not to do it but Lincoln wants him to shoot. Sucre talks him down and they leave after handcuffing the General. On their way out Sucre is captured.
At their hideout Sara tell Michael Lincoln needs a hospital. Michael leaves Kellerman a voicemail saying "you better come through for us in the end." Christina and several henchmen come busting into the room.
Franco and Wright question Sucre. He refuses to call Michael and is taken away.
As Christina tries to leave with Scylla, Michael holds her at gunpoint. When she won't drop her gun he tries to shoot her but the gun misfires. "You were born a Scofield but you'll die a Burrows," Christina says while raising her gun. As she prepares to pull the trigger Sara shoots her from behind. Christina's shot catches Michael in the shoulder. Sara plans to take Lincoln to the hospital while Michael will take Scylla to Kellerman.
On the way to meet Kellerman Michael is grabbed by two armed men. They take him to a conference room where Kellerman walks in with a representative from the UN. Kellerman says Lincoln, Sara, Sucre and Mahone will all be exonerated. The UN attache tells Kellerman a piece of Scylla is missing. Michael seems unsure that Kellerman is on the up-and-up and wants to know the UN rep's contact. Kellerman reassures him that everything is fine and Michael eventually reaches into his pocket and pulls out the missing piece. The man from the UN confirms that Scylla is intact and says "I'll make the call." Kellerman tells Michael: "You did it. It's over."
The General is able to pick his handcuffs as police enter the loft and place him under arrest.
Christina's body is covered by a white sheet.
Michael, Lincoln, Sara, Mahone, Sucre and C-Note sign papers with Kellerman. Everybody exchanges hugs and smiles as the music swells. Kellerman tells them Mahone's wife, Sofia and L.J. are all safe. He asks whether T-Bag should also be exonerated. They say no and T-Bag is hauled away.
Michael and Sara walk along the beach discussing parenthood. They tell each other how happy they are and hug.
FOUR YEARS LATER
Mahone (who is dating agent Lang), Lincoln, and Sucre are all leaving their respective loved ones for two days.
We see that Self looks to be in a vegetative state. C-Note is enjoying suburban life and Kellerman has been elected to Congress. The General is executed and T-Bag is back in prison.
Cut to Sara with her son. She says "you ready to go see daddy?" They meet up with Lincoln, Mahone and Sucre at (gasp!) a cemetery. The son places flowers on the tombstone and Lincoln sticks a an origami swam on top. Everyone walks past the grave to a beach and we see the inscription:
"MICHAEL J. SCOFIELD: 10.8.1974 11.4.2005.
Husband, Father, Brother, Uncle, Friend
Be the change you want to see in the world"