The story starts off with Sara being arrested for the murder of Christina Scofield, during her and Michael's wedding party. At the female penitentiary, some new characters are introduced, along with returning character Gretchen. Right at the beginning of her jail time Sara is mauled by the COs for having left the door open for Michael years earlier.
Across the yard is a neighboring men's prison, where General Krantz and T-Bag are being held. Receiving word of Sara's incarceration, Krantz puts out a $100,000 bounty on Sara's head. Sara is quickly poisoned, but is given medical treatment.
Michael soon learns of the bounty, and decides that he must break her out. He once again enlists Lincoln and Sucre's help. Lincoln and Sucre stake out the prison, taking photographs of the cameras and creating a rough layout of the prison. Gretchen sees Lincoln and Sucre, and forcibly asks Sara to include her in any escape plan that may be developing.
After meticulously analyzing the photographs and plans of the prison, Michael finds a fault in the security system. Mahone then arrives and offers his aid, although his true intentions are unclear, as he had just been offered reinstatement with the FBI on the condition that he find and report any evidence incriminating Michael.
Michael exploits the fault to come up with an escape plan, which he relays to Sara using a hidden message written in a letter. While he is out however, FBI agent Wheatley breaks into Michael's apartment, and sees the plans laid out on table. When Michael arrives, he points out that the plans look very incriminating, but Michael claims that he was merely looking for any faults, so that he could describe them to the prison warden, in the hopes that she may grant him visitation rights.
Visitation rights are eventually granted, so Michael visits Sara and, because the visit is supervised, subtly asks her if she understood the hidden message, which she implies that she does. However, just after leaving the prison, Michael finds out that Agent Wheatley also discovered the fault which Michael planned to exploit, and sees the camera system being adjusted, putting a halt to the escape plan.
Meanwhile, Sara joins the "family" of the leader of the prisoners, an inmate who goes by the name of "Daddy", in order to join the work detail and gain access to the yard.
Michael soon comes up with a daring plan which Lincoln strongly recommends against, to somehow parachute right outside the Prison Yard and rescue Sara. Realizing the difficulty of such a task, Michael asks Lincoln to enlist the aid of T-Bag. Since T-Bag would clearly be holding a grudge against Michael, Michael tells Lincoln to offer him a reward of $5,000. During the meeting, T-Bag demands a more money than the brothers can provide. But, since the General refused to provide any financial incentive for T-Bag's help, T-Bag tells Lincoln how he can rob the man holding the General's $100,000, in exchange for his help. Lincoln agrees to steal the money, and tells T-Bag to simply pull the fire alarm at the right moment. Lincoln and Sucre then proceed to rob the money holder and set up the fund transfer to T-Bag.
Wanting to get to Sara, Gretchen persuades one of the guards to search Daddy's room. The Guards do so, and, finding drugs in the trash can, take Daddy to lockup.
While waiting near the showers, Sara is attacked by a fellow family member but Gretchen comes to her rescue, killing the attacker in the process. Gretchen then pleads with Sara to include her in the escape because she wishes to see her daughter, Emily, and give her a gift. When one of the guards tells Daddy of the death of her family member, and mentions that Sara and Gretchen are thought to be behind her killing, Daddy becomes infuriated.
Following several phone calls with Agent Wheatley, in which Mahone divulged Michael's parachute plot, it appears that Mahone has betrayed Michael. But Michael continues to trust him, and gives him a piece of paper and a DVD which he says to give to Sara, in the event of his death. Michael then visits Sara once more, telling her that the previous escape plan was now impossible. But he cryptically tells her of a new plan, in which she must get to the chapel, which is linked to the outside via an underground connection to an administrative building.
Daddy is eventually freed from lockup, and appears to be stalking Sara and Gretchen. Just before the escape begins, Gretchen distracts a guard, and Sara confronts Daddy. Following a short explanation, Sara picks a fight with Daddy and purposely pushes her into a powerful and frightening inmate, who then retaliates by attacking Daddy. At the same time, Gretchen punches the guard and knocks her to the ground, but gets stabbed in the leg during the altercation. Sara quickly grabs the guards' keys, and the two of them hide in the kitchen amidst the chaos.
Michael then begins the escape. Knowing of the plan thanks to Mahone's information, agent Wheatley orders all lights to be shut off, and positions armed officers near Michael's landing site. When the parachute lands, it is riddled with bullets. However, Wheatley discovers the parachutist is revealed to be a dummy. Michael is then seen sneaking out from under Wheatley's car and running into the prison.
With the escape underway, Gretchen admits to Sara that she cannot continue on without help due to her injuries. Gretchen then asks her to choose, either to leave her behind or help her. Sara chooses to help Gretchen because she rescued her during the attack. However, as they run to the chapel, Gretchen is spotted by guards. She is asked if she's alone but Gretchen refuses to divulge Sara's presence and stalls the guards by telling them she just wanted to be with her daughter. Though Sara is almost spotted by a guard, she manages to unlock the door and get into the Chapel. At this point the guards are recalled and Gretchen is again taken into custody. Sara then sees the necklace that Gretchen made for her daughter on the ground, and knowing that she got away thanks to Gretchen, picks it up so that she may pass it on to her daughter.
Michael finally meets with Sara, and they sit, waiting. Sucre is supposed to transfer the money to T-Bag's bank account, but sees that the bank is closed. When T-Bag finds out that the transfer did not take place as promised, he angrily reveals the plot to the warden, and tells her that he was instructed to pull the fire alarm. The warden responds by turning all fire alarms off.
This however, turns out to be part of Michael's plan, as he figured that T-Bag would reveal the plan. With the alarms off, he then burns through a locked door with a blowtorch, managing to force it open. However, when they try to escape through the next door, which is electronically locked, they discover a roadblock. Knowing that this was a possibility from the beginning, Michael asks Sara to run as soon as the door opens and leave him behind, since the only way to open the door is to manually cause a power surge that will certainly kill him. Sara refuses to leave if Michael cannot go with her, but he emphasizes that there is no other way, touching her stomach and saying that he will be going with her. In one final act of sacrifice, Michael causes the surge, and sparks are shown coming from the fuse box. Sara then runs out, with Lincoln, Sucre, and Mahone waiting with a van just outside. Stunned, Sara is unable to describe to Lincoln what just happened. Mahone, who purposely misled the agents, revealed that he knew of Michael's plan from a previous discussion, and simply tells Lincoln, "He's Gone". They get into the van and drive away, still shocked over Michael's fate.
Back at the prison, T-Bag is put into solitary confinement for aiding Sara's escape since he told the warden to shut off the fire alarms.
Mahone finally gives Sara the paper and the DVD which Michael left for her. The paper reveals a medical exam which Michael recently underwent, revealing that his brain tumor had returned, and that his condition was terminal. Finally, Lincoln and Sara sit in a boat, and view the DVD. It is a prerecorded message in which Michael explains his motivation for sacrificing himself, tells Sara and Lincoln that he loves them, and asks them to watch over each other. The video, and the entire series, culminates in Michael's final proclamation: that they are all, finally, "free."
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