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Michael, Linc, and Nika are captured by Bellick and Geary, who intend to retrieve Westmoreland's money in Utah. Tweener continues his drive with Debra Jean. Abruzzi is reunited with his wife and children and is set to flee the country with them, but decides to take care of Fibonacci first. T-Bag has a close call with the police at a Nebraska gas station, and then poses as a Marine who lost his hand in Iraq. Mahone waits for confirmation of the deaths of Michael and Linc in the car explosion, and meanwhile gets a lead on one of the other fugitives. Kellerman (posing as a recovering addict named Lance) befriends Sara.

Michael and Linc arrive in Tooele, but the map they need to locate the double-K ranch is missing. They run into T-Bag and Tweener, who have also come to Tooele for Westmoreland's money. Meanwhile, C-Note makes his way by train toward Tooele. Sucre reaches Las Vegas and attempts to halt the wedding of Maricruz and Hector. Sara invites Kellerman to her apartment, believing he is harmless. At the FBI office in Chicago, Mahone reviews files recovered from Michael's hard drive, and begins to piece things together.

Mahone arrives in Salt Lake City, trying to locate exactly where in Utah the escapees are. Michael and Linc hatch a plan with T-Bag and Tweener that will enable them to dig in the right place. C-Note and Sucre meet on the highway and head toward Tooele. Kellerman, in Washington, D.C., briefs Kim. Governor Tancredi phones Sara with a warning.

Michael's plan has hit a snag when the home owner's daughter, a cop, arrives. Mahone argues with Lyle Sands about how to proceed, but ultimately hopes that Tweener, in FBI custody, will reveal the location of the other escapees. Sara is now suspicious of Kellerman, so he tries something different to find Lincoln Burrows. In an Arizona detention facility, L.J. finds out he's to be released the next day; Linc drives to get him. Haywire, in Wisconsin, steals supplies from a camping shop.

Michael tries to retrieve an item from Blanding Botanical Garden in Utah, but Mahone's people got to it first. Mahone believes that someone on his team is leaking information to the press; meanwhile Michael does some research on Mahone at an Internet café, then makes a trip to Durango, Colorado, to see a woman there. Linc and L.J. are on the road in Arizona. C-Note is in Chicago, and Agent Lang tries to use his wife to capture him. Bellick and Geary phone C.O. Patterson, at Fox River, to get information on where they should look for T-Bag. Sara is at a motel in Elgin, Illinois, trying to crack Michael's code. T-Bag arrives in Tribune, Kansas, for (as he puts it) "romance". Kellerman is on the trail of Sara.

Captain Bellick tortures T-Bag for the money during which T-Bag swallows the key and Bellick uses dirty tricks to get the key out.Bellick and Mac leave T-Bag on the boundary of the police.Sarah and Michael Scofield meet,but they are constantly chased by Alexander Mahone.Michael gets close to Mahone's helplessness.Meanwhile Lincoln Burrows and LJ are rescued by Lincon's dad but they are still not shielded from the dirty political games. Sucre tries to contact Maricruz but that plan fails because of the state police doing rounds.

In Maljamar, New Mexico, Michael takes what he needs from a sporting-goods store, then has a crisis of conscience. In Tribune, Kansas, T-Bag narrowly escapes the police but has to leave his hand behind. In Trinidad, Colorado, the three Burrowses discuss politics, but face an unexpected threat. In Gila, New Mexico, Kellerman ties up Sara and resolves to get what he needs from her. Mahone meets Kim for the first time. Bellick receives treatment for the blow to his forehead, and interacts with a local police detective.

Picking up from where we left off, Sucre, Michael, Linc, and Aldo are together, with Mahone on their trail. Sara is face-down in the bathtub as Kellerman prepares to dispose of her body. C-Note is in Harvey, North Dakota with Kacee and Dede, who needs her medication. In Tribune, Kansas, Detective Slattery questions Bellick.

A young couple is choppered to County after a car accident, and one of them has a gun. A boy who wants to be a clown is injured in a unicycle mishap, but his father considers him a mathlete and wants him to go to MIT. Pratt visits Bettina in the hospital, but she tells him off.

In the season finale, an ER patient with a mysterious past is afraid that people are trying to kill him. Dr. Moretti returns, trying to make amends for wrecking the marriage of Abby and Luka. Neela makes her way through a difficult M&M conference. Morris treats a woman with lupus who has an attractive daughter.

A single mother is hurt in a car accident, and must find someone to take care of her daughter. Gates treats a 78-year-old man who refuses surgery that would save his life. Meanwhile Morris's afternoon date with Claudia is not what he expected.

A girl drops off a sick baby at the ER and then leaves; Carter may get a kidney transplant; Gates and Daria care for an elderly woman with multiple sclerosis; Neela and Sam are in Seattle to transport a heart for Joanie Moore, while Doug and Carol are concerned that the donor's grandmother might not consent.