Michael struggles to survive in Sona prison, running afoul of Lechero, the prison's kingpin; and Linc's search for Sara has dire repercussions.
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Michael tries to secure Whistler's safety; and Lincoln investigates Sophia.
Michael runs up against a series of dead ends, and learns more about Whistler; and Lincoln tries to rescue Sara and LJ.
As Mahone begins to hallucinate, and T-Bag climbs in the prison hierarchy, Michael sets an escape plan in motion.
Michael's escape plan almost works, but is ruined at the last moment; a new inmate may know something about Whistler's past; and T-Bag loses his status with Lechero when he defends Sister Mary Francis.
Whistler's accused of murder just before the escape; Mahone's offered a better deal; and Linc and Sofia must drug the guard.
Shifting loyalties abound as Michael and Whistler are forced to fight to the death; Lechero's power is compromised; Linc and Sofia try to save their loved ones; and Susan's mysterious employer is revealed.
Susan makes a last-ditch effort to get Whistler out of Sona right away; and the plan makes everybody else expendable.
A new warden at Sona places Michael in solitary confinement, but eventually offers him hope.
Michael, Mahone, Whistler, and Lechero try to escape through the tunnel; and Lincoln and Sucre underestimate Susan.
As Michael finalizes plans for the tunnel escape, his fellow plotters begin to turn on him; and when Sofia is threatened, Whistler contemplates a betrayal.
Michael, Whistler, and McGrady escape from Sona; but not everything goes according to plan, and the exchange is compromised.
LJ and Whistler are finally exchanged, but more surprises abound; and T-Bag's scheming finally pays off.