Boxed In is the ninth episode of Season 3.
Michael is taken to the guard's office where he is questioned by General Zavala. He asks him about the escape attempt, knowing he was not flying the helicopters, but that he knew who was behind the attempt. Insisting that he knew nothing about the escape plan, Zavala takes Michael and places him in a hot box in the middle of no man's land. The hot box itself is a metal cage with white plastic wrap all around it, with small gaps near the top for air.Just before Zavala leaves, he tells Michael that if he either confesses to the escape plan and take the punishment by law, or take a worse punishment from the Panamanian sun.
Sofia confides to Lincoln that she doesn't trust Whistler any more. There seems to be some attraction between Sofia and Linc. Suddenly, Susan arrives and kidnaps Linc, telling Sofia to go home. Susan takes Linc to LJ, giving them one minute together in order to keep Linc motivated. Linc whispers to LJ that the next time he sees him, LJ shouldn't take his eyes off him, and he'll tell him what to do.
A sorrowful Lang returns Mahone to Sona. She gives him a silver half-dollar - a good luck piece that used to belong to her father. Inside, Whistler promises Mahone he'll be included in an escape plan with Lechero. Meanwhile, Bellick antagonizes Octavio, one of Sammy's new recruits, who later challenges Bellick to a fight to the death.
At a bus stop near Sona, Sucre is surprised to find Augusto, who has another delivery for him to smuggle inside Sona. He's offering no money - but pulls a gun on Sucre when he refuses. As Sucre arrives at work, Zavala is ordering a guard to take Michael a tiny cup of water. The guard doesn't want to do it, so Sucre volunteers. Michael, somewhat incoherent and on the verge of heat stroke, tells Sucre to quit. Sucre refuses; he's loyal.
Lechero - who distrusts Whistler because of his other escape attempt - try to dig up through the secret tunnel, but they need Michael's engineering expertise so it won't collapse. T-Bag sees them sneak out of Lechero's room, past Sammy and his goons.
Michael finally confesses to Zavala that he's been planning an escape since he arrived; he's taken back to Zavala's office for questioning. Michael tells all, though he's not naming names. Zavala isn't sure he believes him, but Michael begs for LJ's sake.
T-Bag tells Whistler he's noticed that he and Lechero have been working together, and suggests it's time to kill Sammy. Meanwhile, Cristobal tries to convince Sammy it's time to kill Lechero. Later, T-Bag tells Mahone to challenge Sammy to a fight and kill him - in return, T-Bag will make sure Mahone gets his drugs. But Mahone ultimately refuses, choosing to go through the withdrawal, which T-Bag says will kill him.
Sucre tells Linc he can't quit his job at Sona - he has to provide money for his kid to Maricruz - unless Linc can help him out. Linc is annoyed; Sucre knows he doesn't have any money to spare. Sucre implies he won't help Linc any more; Linc walks out on him. An operative from the Company overhears the conversation.
Zavala reads in the papers about Mahone's testimony about the Company conspiracy, and begins to believe Michael. Whistler can confirm Michael's story, but will he? Zavala pressures him to give up Whistler's name, promising he'll protect LJ if Michael does so. Meanwhile, Sofia visits Whistler and confronts him about the apartment. Whistler says those fake IDs are so he can get away, with her. He tells her there's a man she can go see - he has a fake passport for her as well, in the name of Estelle Linarte. She visits the man, who gives her an envelope.
Zavala interrogates Whistler; he just needs to know the name of who is in charge of the attempts to free Whistler. When Whistler won't talk, Zavala threatens to torture him. Whistler confesses, but says nobody else is involved. Michael tells Whistler to tell the whole truth. Whistler finally gives up the name Gretchen Morgan - Susan's real name. Meanwhile, Susan meets with Sucre and offers him a job, using his anger at Linc as leverage. 50 grand to go apologize to Linc and stick with him a few more days, and wait for instructions. Sucre meets with Linc - and says his plan worked. Their fight was faked in order to draw Gretchen in to offer Sucre money to spy on Linc.
Michael calls Linc to find out when and where he's next meeting Gretchen, and tells Linc to tell her that all is going as planned.
As Linc meets with Gretchen, Zavala enters to arrest her. Linc is stunned and swears to Gretchen that he had nothing to do with this. At Sona, Gretchen denies all knowledge. Zavala begins to torture her. She knows how to stand up to torture - which just shows Zavala she's not as innocent as she claims. Finally, Gretchen says she's not in charge; her job is just "babysitting" LJ. Just before she is hauled away, Michael whispers that he's going to get her for killing Sara.
Bellick, preparing for his fight with Octavio, sneaks into a room full of paint and turpentine. Just before the fight, he wraps torn pieces of shirt around his knuckles, and shoves tiny wads up paper up his nose. Octavio wails on him, but somehow Bellick emerges victorious. The crowd of prisoners goes wild, cheering for him. T-Bag realizes that Bellick dosed the knuckle wraps with acetone.
Sammy and Augusto meet at visitation. Augusto tells Sammy it's time for him to take over from Lechero, and to open the latest package he's had Sucre smuggle in. Gretchen leads Zavala to a false hideout; LJ's not there. She then gets the drop on Zavala, kills him, and then calls Linc. Meanwhile, Zavala's replacement, General Mestas, arrives at Sona and throws Michael and Whistler back into the prison - much to Lechero's relief, a relief that Sammy notices.
General Zagala said that he could order his men to search for LJ but when he accompanied Gretchen, he only has one man with him.
- "What was shaping up to be the best episode of the season falls a very long way. Those who have feasted on a diet of 24 may be used to this kind of flimsy plot twist. Perhaps I was foolish for believing Prison Break could buck the trend and follow through on eight episodes of competent bad guys."
- ―The TV Critic's Review