Michael's plan to escape has failed. While Lincoln is strapped to the electric chair, he sees an oddly familiar face in the crowd. Is there one last hope to save Lincoln's life, or has his journey reached an end?

Flashbacks provide exposition on how the inmates arrived at Fox River Penitentiary from The Company's framing of Lincoln to the creation of Michael's plan to save his brother's life.

Improvising a new plan, Michael seeks out an acquaintance who may hold the key to his escape plan. In gen pop, the other members of the P.I. crew learn that the guards are auctioning Michael's cell to the highest bidder. Lincoln and Sucre devise a scheme to get Michael returned to gen pop. Veronica informs Lincoln that L.J will be tried for his mother's murder, and Lincoln desires to see his son.

After the crash Kellerman tries to suffocate Lincoln, but he is saved in the last moment by a stranger. Sucre leaves solitary confinement and Michael tells to his partners that he has completed the map, but he needs the key to the infirmary. Abruzzi is back to Fox River, apparently converted into a religious man. Warden Pope sends Captain Bellick to find Lincoln before notifying the authorities. Nick tries to convince Veronica that they are losing time checking the calls of Quinn's cell phone. Michael kisses Sara and asks her to wait for him. Tweener is in trouble with Avocado and he castrates the abuser. Lincoln sees that the stranger is actually his father, and he explains that he worked for the powerful Company and Lincoln is a victim of a big plot against him. He had leaked information of EcoField and they used Lincoln to force him to show up. Michaels asks for help from Nika. Veronica finds many calls from Montana on Quinn's phone. The Vice-President tells her brother that he is alive just because of her, and he replies that he does not understand how they have not killed her yet. Abruzzi meets T-Bag and asks him to forget everything, and they make a truce. Nika seeks out Sara and tells her about her life and how Michael helped her, but she actually steals Sara's key. A guy sees the Mustang in a junkyard where Aldo and Lincoln are hidden, but Kellerman bugs the conversation and goes to the spot. However, the police arrive and Captain Bellick arrests Lincoln, saving him from Kellerman. Sara seeks her key and recalls her meeting with Nika Volek; she calls maintenance service to replace the lock. Nick works for Abruzzi. Michael invites David and he betrays the plan to Captain Bellick. Lincoln is back to Fox River under 24 hours surveillance.

Westmoreland uses Bellick to plug a hole in the escape plan, which forces Michael to move up the breakout timetable. A fearful Tweener pledges his loyalty to Michael and in return may get out of jail for free; Michael feels that he has no choice but to involve Sara in the plan and must betray his father figure; and Veronica finds her life in jeopardy from her closest ally, who has a surprising connection to a Fox River inmate.

The team start the escape from the hole in Scofield's cell.

As the escape continues, lives are lost and Pope and Bellick do everything in their power to capture the convicts.

With hospitals and clinics under surveillance, Michael brings Lincoln to Nika's home to heal his wounded leg. Then he returns to the place where he parked his Accord and finds that the car has been towed. Meanwhile agent Mahone retrieves Michael's backpack with his passport from a vagrant that broke the rear window of Michael's car to steal the backpack. Michael goes to Brewster Towing yard to recover his car. Meanwhile Sucre finds that Maricruz will marry Hector in a couple of days and he heads to New York in a stolen car. Sara is arrested and her father visits her, pays her bail and orders her to tell a fake version about the incident in Fox River since he will be the next Vice-President of United States. Later she goes to rehabilitation where Kellerman is pretending to be an addicted patient. C-Note schedules a meeting with his wife, but his conversation is bugged by agent Mahone. Bellick and Geary meet each other by chance and later they team-up to get the $400,000 reward for capturing Michael and Lincoln. They go to Fox River and Bellick interrogates Manche Sanchez, who discloses the plan of the fugitives. Michael and Lincoln forge a car accident to escape from Mahone, but they do not see that Bellick and Geary are in their tail.

Captain Brad Bellick walks in the FBI office demanding Mahone pay him. Michael and his companions are impressed with the recordings on the stick, but it only helps if Kellerman's contacts in Washington use it right, notably high Justice official Cooper Green, who agrees to meet and cooperate, but is tailed by Kim's men. Linc calls his boy L.J., who refuses to give up his relatively normal life till further notice. Sarah meets Bruce Bennett. Bellick tries to bribe Sucre's incarcerated cousin into betraying his Mexican whereabouts. T-Bag finds therapist Dr. Stammel who looks like him, and murders him to steal his identity. Mahone is ordered to dispose of C-note for good once Kim believes he has Scofield; he promises to keep taking care of C-note's family, but only if he uses the content of a package he'll send to his cell- a noose. Sarah is too late calling Linc the real Cooper Green is in his office, but Michael tricks the fake one who pretended to be asthmatic just in time and knocks him down. Paul Kellerman visits his sister Kristine. Fernando Sucre is in heaven in bed with Maricruz Delgado when their baby kicks. The real Cooper Green could help with the tape, but then finds the memory stick has the copy date, not the recording date without which it is not admissible as proof, only to blackmail the president into signing a pardon.