Michael Scofield is a desperate man in a desperate situation. His brother, Lincoln Burrows, was convicted of a crime he didn't commit and put on Death Row. Michael holds up a bank to get himself incarcerated alongside his brother in Fox River State Penitentiary, then sets in motion a series of elaborate plans to break Lincoln out and prove his innocence. Once out of jail, their perils aren't over - the brothers must flee to escape recapture and battle an intricate political conspiracy that puts everyone's life at risk.
As Lincoln Burrows awaits his fate on death row, his brother Michael Scofield hatches a plan to get himself incarcerated in the hope of freeing his innocent brother from the inside.
Michael must find a way get into the infirmary to carry out his escape plan, and searches for a drug that will allow him to fake diabetes.
Michael hatches a plan to test if he can trust Sucre, and offers Abruzzi a deal. However, his escape is disrupted by the arrival of an unstable new cellmate.
Michael's unstable new cellmate seems reluctant to join the break-out scheme. Sucre changes his mind about the escape when he learns his fiancee is going to leave him.
The Secret Service puts pressure on Pope to transfer Michael to another prison, and the escapees have a critical decision to make regarding their plan.
Michael sabotages the air conditioning, which sparks a riot that puts Sara's life in jeopardy. Nick gives Veronica vital information.
Michael protects Sara, but the arrival of the National Guard slows his progress. T-Bag is left with the hostage as Abruzzi and Sucre work on the wall.
Michael discovers a key building on the escape route has been converted into the guards' break room. Veronica finds herself targeted by the agents, who also go after Lincoln's son.
A new inmate grabs T-Bag's attention, while Bellick warns Abruzzi his monthly payment has not arrived. Still on the run, LJ is followed by the agents as he tries to find Veronica.
Michael and Abruzzi try to get back into the guards' room before the escape hole is found. Kellerman and Hale receive unwelcome help in tracking down LJ.
Michael is asked to add one more to his escape team, and is paid a visit by his wife - much to the surprise of his brother.
The group learns there are too many members for the escape to succeed, and two of them consider using Michael's plan to abscond early. LJ sees a notice for his mother's funeral.
With Lincoln in solitary confinement, Michael tries to delay the escape, but the others insist they follow their original plan. Veronica arranges to meet her informant.
The thwarted escapees scramble back through the tunnel and return to their cells. Veronica and Nick ask a judge to postpone Lincoln's execution, but their efforts seem in vain.
Lincoln's execution is delayed when the judge learns of concerns over the identity of the victim. Michael considers a new plan, but the others fear it is too risky.
Flashbacks reveal the inmates' past and events leading up to Lincoln's arrest, recounting how the jailbird considered carrying out a murder to repay a debt.
Michael is placed in solitary confinement after refusing to tell Pope how he burnt his back, while the rest of the escape team struggle to cover the hole in the guardroom.
Michael tries to make Haywire remember his tattoo, but the sociopath does not recognise him. When the old cell is auctioned off, T-Bag and C-Note worry the hole will be discovered.
Agent Kellerman uses the crash as an opportunity to kill Lincoln, only for the convict's father to save him. Inside Fox River, Abruzzi's unexpected return grabs T-Bag's attention.
Bellick's discovery of the hole under the guards' room brings the escape plan forward, forcing Michael into desperate action. Abruzzi plots revenge as he organises the plane.
With Bellick tied up and Pope taken hostage, Michael starts the escape. However, without a key to the infirmary door, the plan relies on Sara's help. Westmoreland's injury grows worse.
Veronica heads to the Vice President's hideaway as her foe learns her company funding has been withdrawn. The escapees try to avoid being captured.