The Rat is the 14th episode of the series. The episode directly follows where the previous episode ends with the protagonist Michael Scofield's failed escape attempt and the impending execution of his brother, Lincoln Burrows.
The escape team realizes that Michael's plan has failed. After a futile attempt to break the newly replaced pipe, the pole that they were using to break the pipe snaps into two instead. As the broken half of the pole drops to the floor, a guard hears the noise. The escape team hides as the C.O. walks in. After he leaves, the team sneaks back out to the guard's break room.
Captain Bellick, about to go off shift, checks in on them. Westmoreland, being older, doesn't make the trip in time. The others say they can't clean out the mold overnight. After insulting them, Bellick then instructs the guard to take them back to their cells. He suddenly realizes that they were a member short. He goes back in, but finds Westmoreland in the room, crouched down tying his shoelaces. The team are sent back to their cells.
Sucre and Westmoreland console Michael by telling him not to worry about them and that Lincoln would know about Michael trying to help him. Westmoreland also expresses sorrow that his brother will have a few weeks of torture - the waiting for death is worse than death. It turns out that if there is a system failure of the electric chair, the inmate gets a three week reprieve when the system is being repaired. Michael takes that as salvation rather than torture. He goes into the tunnels, and with food as bait, captures a rat.
Tweener and Bellick are conversing. Tweener is dipping his french fries into a milkshake, just like Bellick. Bellick wants information. Tweener doesn't have it, but when Bellick charges him $100 for the hamburgers and other food, Tweener reveals the conversation between Michael and Westmoreland regarding the procedure of the chair. Bellick says they are even.
Bellick orders another check on the electric chair, and it fails. Upon further check, they find a rat has short-circuited the chair. The tech said they will have to make a report, but Bellick bullies him into just changing the fuse and forgetting the technical problem. Later, the system works perfectly as Michael watches in horror as the lights flickers.
Michael gets final visitation with his brother. Lincoln does not want to talk about the appeal and he tells Michael that the execution is going to happen. He doesn't want to think about it. Defeated, Michael consents. They play a game of gin as Lincoln eats the blueberry pancakes he had requested as his final meal.
Meanwhile, Nick and Veronica appeal to the judge for Lincoln's exoneration but is denied. After Michael's plea, Dr. Tancredi goes to speak with Veronica and Nick. She then takes with her the information they gave her to ask her father, the Governor, to review Lincoln's case. The governor promptly tells her that the inmates are trying to use her and that being strict on crime is what he was elected for. Knowing that she couldn't convince her father any further, Sara tells him to review the information she just gave him and pretend that it didn't come from her.
As the Warden and several guards walk with Lincoln to his execution, the governor calls. After a tense minute, as Michael, Lincoln, Veronica and Sara exchange glances, the warden reveals that the execution will go ahead. As the governor hangs up, the Vice President appears behind him and tells him that his decision will not go unnoticed.
The group proceed to the death chamber. Surprisingly, Bellick shows some compassion and allows Veronica over the yellow line to hug Lincoln before he is taken into the chamber. In a heartbreaking moment, Veronica tells Lincoln that she has loved him since the moment she first saw him. At the warden's order, Bellick uncuffs Michael, who takes his turn to hug the brother he is about to lose. Tears roll down Michael's eyes as his brother is led into the death chamber. The episode closes with Lincoln facing the chair.
- The Rat refers both to the rat that malfunctioned the electric chair and Tweener 'ratting' to Bellick about Michael's attempt to delay the execution.
- Upon its return, the series was allocated to an earlier time slot than before the mid-season hiatus; as a lead-in program for the more popular television series, 24, which now occupies Prison Break's previous time slot at 9:00 pm EST. The episode obtained an average of 10.3 million viewers and a rating of 4.3 in the 18-49 demographics.
- This marks the first episode where John Abruzzi didn't appear.