As the gang deals with Don's betrayal, Linc is captured; and Don forces Gretchen to help him find a new buyer for Scylla.

As the gang realizes that Don has betrayed them, Don — watched by T-Bag — disposes of Trishanne's body. Don calls Herb Stanton: he claims to have been ambushed and shot by Michael and Lincoln, and that the brothers killed Trishanne as well. He then fires his gun, and pretends that the brothers just got him as well. He then gives T-Bag a choice: help him find Gretchen, or die. T-Bag elects to help. Michael calls Homeland Security, asking for Don Self, but hangs up when asked who's calling. Does Homeland know where they are? They need to run, but Michael needs medical attention. Pad Man — from here on in to be referred to by his true name, General Jonathan Krantz — addresses the Company. Scuderi challenges his authority and judgment… and General Krantz shoots him dead, taking his Scylla card. He then orders that Scylla be retrieved today.

At the warehouse Michael hides something in a hidden compartment. Stanton and two Feds arrive… but find the warehouse empty. The gang is at the harbor in the SUV. The phone rings; it's Stanton, accusing them of killing Don and Trishanne. Michael realizes that Don set them up. Stanton orders them to turn themselves in, or be hunted down. The gang holes up in a cheap motel. Sucre wants to run to Mexico, but Michael wants to finish the job, and bring down the Company by exposing Don and retrieving Scylla. Sara tries to call Dr. Malden, but Michael stops her. On TV they see a news report about the massacre at GATE, and realize that Don's plan must be to sell Scylla, using Gretchen to find a buyer. They need to find Gretchen before he does. General Krantz also puts his men on alert to look for Gretchen. Lisa confronts him about his murder of Scuderi, but he is unsympathetic to her concerns.

Sara once again injects Michael with a drug to ease his condition, and tells him to avoid stress for the next eight hours… unlikely as that may be. She recommends running to Mexico as Sucre suggested, but Michael refuses. Linc waits with the others at a pay phone; Gretchen calls. She doesn't know where Scylla is, and says Don will be looking for a new buyer. We see that she's at the safe house, where she's just discovered the body of the previous buyer, Feng. They make plans to meet at the park in an hour. Gretchen's phone rings again; it's her sister Rita. She's been taken hostage by Don, who tells her, "It's time to come home." Senator Dallow wants to organize a manhunt to catch Michael and the gang, but Stanton insists on continuing to operate covertly; they signed off on Don's plan, and they'll lose their jobs if they expose what they signed off on. Richard Sooter of the US Marshals Service arrives. He's investigating the Scofield/Burrows Supermax story; it's about to become a Congressional matter. He says he can help if there's a good reason they're keeping secrets. They decide to trust him.

As the gang stakes out the park, waiting for Gretchen, she arrives at her sister's house. Don demands that she find him a new buyer for Scylla. He also wants to know where Michael and the others are. She claims not to know… until she sees T-Bag holding her little daughter, Emily. Michael calls Stanton to ask for reinstatement of the original deal for their freedom if he can prove Don has Scylla; but instead the Feds arrive at the park, including Stanton and Sooter. They've been set up. Linc is caught; Michael escapes. Linc is interrogated, and points out that they could have run to Mexico: Why would they have taken Stanton's call, and jeopardized their freedom, if they were guilty? Gretchen tells Don about Vikan, a conduit to another buyer. There are only about five potential buyers in the world. It’s time to go, but Don has T-Bag stay behind. Gretchen warns T-Bag not to harm Emily. Rita, feeling betrayed, slaps Gretchen. Gretchen she's going to fix this. Back at Homeland, Senator Dallow tells Linc they've found deleted files on Don's computer confirming Linc's story; including details of the new identity, Robert Walker, which Don plans to use. They want Linc's testimony and the testimony of the others in exchange for full immunity. Linc doesn't expect the others to trust Dallow and willingly come in. Dallow says the only other option is to rot in the Supermax. At the motel Sucre reveals that his daughter's baptism is coming up; he thought he'd be able to go. Linc calls and offers the deal, and Senator Dallow gets on the phone to confirm. Michael plans to rendezvous with the Senator and hear him out, but he sends Sucre and Sara ahead to the meeting place to keep an eye out. Mahone and Michael will double back to the warehouse, and follow the Sentator to the rendezvous. Sara promises that no matter what happens, nothing will come between her and Michael; not like her mother, who was alienated from her father because he was always crusading for justice, and taking on other people's problems as his own. They embrace.

Gretchen tells Don that even if he succeeds, he's going to end up all alone. Don calls T-Bag, and tells him to get out his gun and point it at Emily. He then tells Gretchen that he wants the money and to be on a plane by the end of the day, or her family dies. Gretchen gets a text with an address; time to meet the conduit to the buyer.

Sara and Sucre arrive at the address Michael gave them, but it's not the rendezvous point. Mahone arrives, and says that Michael's safe. Michael's sent them to a bus station so they can get away. Michael goes to the warehouse to meet with Dallow and Stanton. Linc's there, no longer cuffed. Dallow and Stanton confer at the docks. Stanton points out that the two of them will get jail time: fifteen years just for conducting an unauthorized operation without Congressional approval. He convinces a weary Dallow that it's time to switch from containment to excision. They re-enter the warehouse, and demand to know the whereabouts of Mahone, Sucre, and Sara. Michael says they're not coming; the deal he'll make is his and Linc's testimony is exchange for the freedom of all of them. The brothers' testimony should be enough to put Don away. Stanton pulls a gun on Linc. Michael says he can get them Don and Scylla. At the mention of Scylla, Sooter reacts. Stanton says he no longer cares about Scylla; the choice is between the mission, and just ending everything now. He has Sooter escorted out now that he knows the answer to his Supermax question. Stanton holds a gun to Michael's head, and gives him five seconds to talk… but after two seconds, a shot rings out. Sooter has shot Stanton dead. He un-cuffs the brothers, and then takes them and Dallow hostage. They've got an appointment with the General.

Gretchen and Self meet with Vikan. They are surrounded by men with semi-automatic weapons; Gretchen tells Don this is how things are done. After they are patted down they speak with Vikan, who says that the General has offered a reward for Scylla's return… along with the heads of the thieves. Just as they think a double-cross is in the air, Vikan says he's glad to have a chance to kick the General in the teeth. Don hands Scylla to Vikan to examine.

As Sooter leads the brothers and Dallow out, he is ambushed by Sucre. Linc takes Sooter's gun. Sooter goes for another gun, but Linc shoots him dead. Linc then levels his gun at Dallow, who says that Stanton outranked him; he didn't want to kill them. Michael demands he help them get their deal back. Dallow refuses, but he does give Michael a folder with the last remnants of the covert operation. Once it's gone, so is all evidence of the case against the Company. Dallow leaves, and Michael has Linc let him go. Sara and Sucre arrive. Mahone's gone; he got on the bus. Don regards his wedding ring, and then slips it into his pocket as Vikan closes a silver briefcase. He tells Don that they can do business once Don has "the rest of Scylla." Don is nonplussed until Vikan shows him a missing piece at the base: a 2x2 plastic component. We see Michael at the warehouse, going back to the hidden compartment where we previously saw him hiding something; he retrieves it: It's the 2x2 plastic piece. Don calls Michael, and says: "I believe you have something that belongs to me." "Come and get it," says Michael.