Michael Scofield is imprisoned in Fox River State Penitentiary. He finds his brother, Lincoln Burrows, who is a death row prisoner, and tells him that he is going to break them both out of the prison.

C-Note overhears Michael and Lincoln discussing that there are too many fugitives for available time and they share the information with the group telling that one shall be left behind. T-Bag feels threatened and calls his cousin James Bagwell, disclosing the escape plan and asking James to call the Warden Pope in case T-Bag does not contact him later. Abruzzi asks his outside man to kidnap James, but things go wrong and the mobster kills James and his five year old son Jimmy. Abruzzi feels guilty for the death of the child and feels the need of God's forgiveness, but T-Bag betrays Abruzzi like Judas. Meanwhile Veronica and LJ bring Nick to the hospital and while in surgery, LJ escapes to see the funeral of his mother. Daniel Hale sees the teenager in the cemetery but he does not arrest him; later he tells his wife that they should move West and makes an anonymous call to Veronica scheduling a meeting in the Highland Cafe. Maricruz tells Sucre that she is pregnant but she will marry Hector. Captain Bellick presses David to rat Michael, reporting everything he says. Michael tests the escape plan and informs the group that they are ready to go that night, but Lincoln was sent to solitary confinement protecting his brother.

Westmoreland uses Bellick to plug a hole in the escape plan, which forces Michael to move up the breakout timetable. A fearful Tweener pledges his loyalty to Michael and in return may get out of jail for free; Michael feels that he has no choice but to involve Sara in the plan and must betray his father figure; and Veronica finds her life in jeopardy from her closest ally, who has a surprising connection to a Fox River inmate.

The team start the escape from the hole in Scofield's cell.

As the escape continues, lives are lost and Pope and Bellick do everything in their power to capture the convicts.