Lincoln and C-Note travel to Yemen. They find Michael using a new identity: – a notorious terrorist for ISIS, but he’s actually undercover. Michael has amnesia? No – he faked his death to protect everyone from a new enemy: Poseidon , a rogue CIA operative.
The target is – a high-tech data drive containing The Company’s secrets (black ops, assassinations, energy tech). The team, now a government-authorized "cell," pulls heists to collect six cards needed to access Scylla. Betrayals occur (Whistler is killed; self-serving Don Self steals Scylla). all prison break seasons
The brothers clear Lincoln’s name when Steadman (faking his death again) is exposed. Mahone kills Tweener. T-Bag buries the money but marks its location. The season ends in Panama: Michael turns himself in to protect Sara (his love interest and the prison doctor’s daughter) and is sent to Penitenciaría Federal de Sona – a brutal, riot-torn Panamanian prison. Lincoln is framed for murder again but escapes. Sara is kidnapped. Season 3: "The Prison in Hell" Plot: Season 3 is shorter and takes place entirely in Sona , a prison where inmates run the show and guards only watch from outside. Michael is trapped inside. The Company forces him to break out a dangerous criminal named James Whistler in exchange for Sara and LJ’s safety. Lincoln and C-Note travel to Yemen
Plot: Structural engineer Michael Scofield robs a bank to get himself incarcerated at Fox River State Penitentiary. His goal: break out his older brother, Lincoln Burrows , who is on death row for allegedly murdering the Vice President's brother, Terrence Steadman. Michael believes Lincoln is innocent. No – he faked his death to protect
After 22 episodes of close calls, tunnel digging, and a riot, Michael and five others escape just before Lincoln’s execution is halted. However, is caught, and Abruzzi is shot. The remaining five (Michael, Lincoln, Sucre, T-Bag, and C-Note) flee into the night. Season 2: "The Manhunt" Plot: The escapees are now fugitives, hunted by FBI Special Agent Alexander Mahone , a brilliant but troubled profiler who is secretly working for The Company. Mahone is able to anticipate Michael’s moves by studying the tattoos.
The rescue goes wrong. The Company sends Michael a box containing what appears to be Sara’s severed head (actress left the show, later retconned). Grieving but focused, Michael engineers a chaotic prison riot/escape. Whistler gets out, but Michael is shot and left for dead. He survives, but the season ends with him walking away from Lincoln, consumed by rage and grief. Season 4: "The Final Break" (Originally) Plot: Michael and Lincoln discover Sara is actually alive (her head was a fake; the real victim was another woman). They team up with former enemies (Mahone, Sucre, T-Bag, Kellerman) to take down The Company from the inside.