Michael uncovers unbelievable news when he seeks revenge for Sara’s death; Michael and Lincoln receive an offer from Homeland Security that they cannot refuse; Mahone suffers a devastating loss; and T-Bag is deserted during his flight to freedom.

Michael goes to Los Angeles, planning to kill Gretchen and Whistler in revenge for Sara's death. He infiltrates a fancy party that Gretchen and Whistler are also infiltrating, with Mahone waiting for them in the car. Whistler gets a data card from a man named Jason Lief, who stole the card from the Company. Lief thinks Whistler is on his side, but Whistler promptly shoots him dead. While Gretchen is distracted, however, Whistler surreptitiously makes a copy of the card. As soon as he finishes, he's confronted by Michael, who’s holding a gun on him. Gretchen enters, but Michael's got both of them covered. Talking fast, Gretchen tells Michael that Sara is actually alive; she escaped, and all Lincoln saw was a head from a cadaver. Stunned and unbelieving, Michael relents… just as the guests at the party find Jason's body. In the panic Whistler and Gretchen escape, though on the way out Whistler secretly passes the copy of the data card to a silver-haired attendee: Tuxhorn, a Company man.

The next day Gretchen meets with Pad Man in a deserted stretch of desert. He tells her she failed in her mission; the card was a duplicate, and Whistler still has the original. He angrily lays the blame at her feet for involving Whistler in the first place. Then Wyatt, a large, imposing assassin, emerges from Pad Man's limo. As Gretchen begs for her life, Wyatt levels his gun at her. Lincoln is in Panama with LJ and Sofia. Michael calls, and Linc tells him that Sona recently burned to the ground in a riot; no word on what happened to T-Bag, Bellick, and Sucre. Michael tells Linc that he thinks Sara is alive, and learns that Linc never did see the severed head up close. Hope wells up for Michael for the first time in a long time.

Speaking of Sucre and Bellick, we find them being deposited in Arizona along with a truckful of illegal immigrants. They are met by Bellick's mother, who drives them back to civilization. T-Bag says a genuinely affectionate farewell to Sister Mary Francis. She tells him he could choose to stay, but he's got a blood feud with Michael he insists on settling. He and Sancho, a fellow inmate from Sona, leave with a pair of coyotes T-Bag is paying very well to take them over the border in comfort.

Michael gets an e-mail from Mahone saying he has information about Sara. They meet on the Santa Monica pier, where Mahone tells Michael that the data card they stole is called "Scylla." It's a little black book that will help bring the Company down. Michael presses him for the info on Sara; Mahone says he understands — he himself wants nothing more than to return to his wife and son — but Whistler's got that information. They meet him in a back alley, where Whistler explains that he can't read the info on the card without breaking into a secure structure. His lost bird book would have helped facilitate the break-in; without it, they need Michael's help. Whistler tells Michael that Sara recently took a bus to Chicago. Michael's ready to leave. Whistler and Mahone beseech him: this is a chance to take the Company down once and for all. Suddenly a gunshot is heard. Whistler collapses dead, shot in the head. Michael and Mahone flee as Wyatt enters the alley, and gets the original copy of Scylla from Whistler's body. He takes it to Pad Man, who entrusts the card to Tuxhorn. Pad Man tells Wyatt to clean up: kill everybody close to Whistler; Michael, Mahone, Lincoln… everybody.

As Michael heads for Chicago, Mahone calls his estranged wife, Pam. To his delight she tells him to come home; even though he's in trouble, even though he's a wanted man. Unfortunately Wyatt gets there before he does. When he finally gets home, he finds his home surrounded by crime-scene tape and police. Mahone is arrested as it sinks in that his wife and son have been murdered by the Company. In Panama, Linc is jumpy. LJ keeps telling him that they're safe now, but he's wrong. A Company agent attacks Linc. Linc manages to kill the man with his own gun, but he's arrested by the Panamanian police.

In Chicago Michael calls the only person he can trust: Bruce Bennett. While he's on the phone asking for news of Sara, two cops recognize Michael, and arrest him. He is taken to meet Don Self, a Special Agent with Homeland Security. Don has been investigating the Company for years. He offers to get Michael out of doing time in exchange for obtaining Scylla; he’ll also get Linc out of jail: Don made a deal with the Panamanian authorities for Linc to serve out his time in the US. Michael's still not interested, especially since he'd be doing this job unofficially: if Don tried to run the operation through higher-ups, chances are at least one of them would be a Company agent. Don plays his trump card: a handwritten note from Michael's father, who (says Don) spent the last two years of his life trying to get a hold of Scylla in order to bring the Company down.

Bellick takes Sucre to a hospital in Chicago, where he meet’s with Maricruz's sister Theresa... who is holding Sucre's newborn son. As a tearful Sucre holds the infant, he realizes there are undercover cops waiting for him in the next room. He's being set up. Theresa tells him he can't keep dragging Maricruz down; he needs to serve his time. The second he's safely handed his son back to her, he tries to flee, but he and Bellick are caught. T-Bag tells the coyotes about his feud, and that the bird book will lead him to Michael. The coyotes are more interested in T-Bag's large sack of money. They take a tire iron, and rob him, leaving T-Bag and Sancho by the side of the road to die.

In Chicago Michael and Linc are bailed out by Bruce Bennett. They refuse Don's offer, but he gives them their father's file as they go. Bruce takes them to a safe house... where Sara is waiting for them. The two are reunited at last. She explains that when she escaped, she didn't know who to trust, so she reached out to Bruce. He helped her stay in hiding. Michael tenderly gives her back her origami rose. He tells her he's facing fifteen years unless he helps Don. He's horrified to find terrible scars all over her back from Gretchen's torture. Sara begins to break down. She can't live with knowing what the Company does, and will continue to do, to people. Just then a bullet shatters the window. Wyatt's come for them. They all flee. The three agree, and call Don: they're in; all of them. It’s time to end this.

Michael and Lincoln are reunited with Sucre, Bellick, and Mahone; Don's pulled strings to team them all up again. Sucre tells them that T-Bag has the bird book. As Don arranges fake IDs, Michael points out that his tattoos are going to be hard to hide. So the Fox River tattoos are slowly and painfully lasered off, but it makes Michael feel a hundred pounds lighter to finally be rid of them. As Don sees them all off, he warns them against escaping. Michael just tells him to make sure he holds up his side of the bargain. Michael, Sara, Lincoln, Sucre, Bellick, and Mahone are packed onto an airplane bound for Los Angeles.