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.
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.
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.
is revealed to be Jacob , Sara’s new husband. Michael was forced to work for him. The season involves a desperate escape from war-torn Yemen, twists about Michael’s tattoos (new ones hide his identity), and a final showdown in the US.
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).