Season 1: Lincoln was framed for the murder of the Vice President's brother Terrence Steadman by The Company. Steadman is actually alive, hidden in a remote estate. Michael successfully breaks out with seven other inmates (The Fox River Eight), but their extraction plane abandons them.
Season 2: Terrence Steadman commits suicide before he can testify in public. Secret Service Agent Paul Kellerman turns on The Company and delivers testimony that exonerates Lincoln. However, Michael is framed for a murder in Panama and incarcerated in Sona.
Season 3: The Company kidnaps LJ and Sara, demanding Michael break out an inmate named James Whistler. Gretchen Morgan sends Lincoln a box containing what appears to be Sara Tancredi’s severed head to force compliance (later retconned: Sara escaped and the head was a decoy). Michael orchestrates a daytime breakout from Sona.
Season 4: The team joins Homeland Security Agent Don Self to steal Scylla, The Company’s master data matrix. Michael discovers his long-thought-dead mother, Christina Scofield, is alive and a high-ranking rogue Company operative trying to sell Scylla. Michael suffers from a hypothalamic hamartoma (brain tumor). In the standalone television film The Final Break, Michael sacrifices himself by manually creating a high-voltage electrical short to open a secure door so Sara can escape prison.
Season 5 Finale ("Behind the Eyes"): Michael is revealed to have survived; a rogue CIA agent named Poseidon (Jacob Ness, who married Sara during Michael’s absence) faked Michael’s death and forced him to break high-value terrorists out of global prisons under the alias Kaniel Outis. In the finale, Michael outplays Poseidon, proves his innocence through forensic framing, sends Jacob Ness to Fox River (where he is locked in a cell with T-Bag), and is finally reunited with Sara and his son.