Season synopsis
Contains spoilers for this season and earlier seasons.
With Sara alive after the Company had made Michael believe she was dead, Michael and Lincoln are pulled into a deal with Homeland Security agent Don Self: find Scylla, the Company’s encrypted record of its operatives, in return for freedom. Michael, Lincoln, Mahone, Sucre and Bellick use six keycards and a coded blueprint to break into the Company’s headquarters. Their uneasy alliance fractures as Self secretly plans to sell Scylla, while T-Bag works his way into the Company and Bellick dies helping the others cross a trapped water passage. Michael’s brain condition worsens, but he postpones surgery to finish the mission.
The team gets Scylla out, only to learn that the device is more than the Company’s list. General Krantz takes Michael, and Christina Rose, the brothers’ mother, emerges with her own plan to sell Scylla to India and China while provoking conflict between them. Lincoln learns Christina claims he was adopted; Michael and Lincoln reject her attempt to turn them against each other. After Christina captures Lincoln and Krantz holds Sara, Michael uses a decoy and a bomb to disrupt her deal, while Sara escapes Krantz’s custody and shoots Christina when she threatens Michael.
Michael gives the complete Scylla device to Paul Kellerman and United Nations representative Solomon Okella, securing pardons for the surviving team; Krantz is arrested, while T-Bag is sent back to prison. A beach scene shows Michael’s nose bleeding again, leaving his health uncertain. The season then jumps four years: Sara, now with their young son, visits a grave bearing Michael’s name with Lincoln, Sucre and Mahone. Sucre has reunited with his daughter, Lincoln lives with Sofia, and Mahone is with Felicia Lang. Krantz faces execution, while the pardoned Kellerman has become a congressman.