Don and Gretchen, Michael, and the Company are all after Scylla; T-Bag, holding Gretchen's family hostage, has a hard decision to make; and Michael falls into Company hands.

Sara gives Michael another shot to stave off the effects of his tumor, while warning him that he needs to get to a hospital ASAP. Michael wants to get Scylla back first. Linc, patrolling outside, notices that the warehouse door is propped open, and there's a mysterious sedan parked across the street. Inside, Sucre is building some sort of partition. Michael calls Don, and says he's ready to meet. Don says has a better idea… and suddenly a canister of tear gas comes crashing in. The gang tries to run, but they’re cut off by a hail of bullets; Don's on the roof across the street with an M-18. Don orders Michael to come out with his piece of Scylla. Michael tells him to come and get it. Don turns around to load up his grenade launcher with more tear gas… and smashes his face into the barrel of Linc's gun. Don's captured, but he refuses to take the gang to pick up Scylla. As Sucre slips out the back with the partition, Gretchen arrives and points her gun at Linc. Don says he's got a buyer for Scylla, a former Company man who wants to destroy the Company as much as they do, and will pay nine figures. Michael wants to meet him first.

Mahone meets with Felicia Lang, who tells him there's one person at the FBI she thinks can be trusted to help bring down the Company. As Gen. Krantz intensifies the search for Don, Gretchen, and the gang — and T-Bag continues to hold Gretchen's daughter and sister hostage — Michael and Linc discuss the deal. Michael thinks the new buyer will just build a new Company on the old one's ashes: No deal. Sucre texts: "I'm in." He's in Don's car trunk. In the car Don shows Gretchen that they can spy on the brothers via a sonar device attached to one of the tear gas canisters. They can't hear them, but they can see them on Don's laptop. Don and Gretchen arrive at a seedy hotel. Don puts his box of tear gas in the trunk; Sucre is hidden below the partition. He waits for them to leave, and then exits the trunk. He texts the location to Michael, and then takes the box of tear gas.

Michael's building up a tolerance to his shots, and a higher dosage would cause more problems than it would solve. Michael tells Sara he'll do without, but later gives himself another shot. He then hides the little piece of Scylla in the warehouse's washroom. Don and Gretchen see him do it. Don wants to call Vikan, but Gretchen wants to talk to her daughter first. She reassures little Emily that the mean man will eventually go away and never come back; just like the man who used to live with them and yell at her "mommy" Rita. Don grabs the phone, and tells T-Bag he'll call in two hours with the location of the exchange. If T-Bag doesn't hear from Don by then, he should kill Emily and Rita. There's a knock at Rita's door; it's Ralph Becker, a Bible salesman. T-Bag is suspicious of how insistent he is, and then notices the man is wearing a ring: "Southeastern Military Class of 1998." He knocks Ralph out, convinced he is Company, and forces Rita to get rope to tie him up.

Mahone and Lang meet with Special Agent Mark Wheeler; he's been promoted. Mahone thinks he can help Mark get on the short list for Deputy Director. Mark's skeptical of Mahone's story, but says if Mahone can provide credible evidence, he'll take Mahone right to the Attorney General. Lisa hands her resignation to Gen. Krantz, who growls at her that he wanted a son. Hurt, she leaves. Ferguson reports that they've got a satellite image of Gretchen with Don. Ferguson and a team of armed agents are assigned to retrieve Scylla. There are no rules of engagement: shoot on sight. T-Bag beats and interrogates Ralph, who quavers in fear. He seems to be just an ordinary Bible salesman. Ralph says the ring belongs to his little brother, who was killed in Baghdad last year. T-Bag starts to worry that he's made a mistake.

Michael uses PVC pipe to build a "potato gun" in order to be able to fire the tear gas. They go to the hotel, and bribe the clerk to tell them where Gretchen's room is. Inside, Don is talking to Vikan, who says the buyer's touched down. The clerk calls, and warns Don that somebody's looking for them. It’s time to go… which was Michael's plan. Sucre, disguised as a wino, knocks Gretchen down as she descends the stairs. Gretchen rips open Sucre's gunshot wound. Outside, Linc launches tear gas into their room. Self stuffs Scylla into his backpack, and runs out. He sees Gretchen grappling with Sucre, and goes the other way to the fire escape… but it gives way at the bottom tier, because Michael has loosened it. He falls the final 15 feet; as he gets up, dazed, Michael punches him; Don's out. Michael grabs the backpack. Gretchen gets the drop on Sucre, but Sara ambushes her, and hits her with a fire extinguisher. Gretchen tries to run, but is then ambushed by the arriving Company agents. She shoots an agent, and hides in his SUV. Michael suddenly gets dizzy. A revived Don corners him, and is about to shoot him; however, Don is suddenly grazed by a shot from Ferguson. Gretchen suddenly pulls up in Don's sedan; he grabs Scylla, and jumps in. They escape. Ferguson captures the dazed Michael; Linc sees them load him into their van, but he's too late. The van speeds away. Sara and Sucre enter the hotel room, and find the image of the warehouse on Don's laptop. They realize in horror that Don and Gretchen will be heading there to get Scylla's missing piece. Indeed, at the warehouse, Don finds the piece right where Michael put it. Gretchen reaches for her gun, about to betray him, but Don reminds her about T-Bag holding her family hostage.

Michael wakes up, bound in restraints. A doctor injects him with something that makes him pass out; the last thing he sees is Gen. Krantz telling him he's in good hands. He flashes in and out of consciousness as he is worked on by a team of Company doctors. Linc, Sara, and Sucre arrive at the warehouse to find the Scylla piece gone. What can they trade for Michael's release? Sucre's phone rings; it's Mahone. Linc tells Mahone that Don has all of Scylla now, and asks if his friend can do anything to get Michael back. Mahone wouldn't bet on it. Linc tells Mahone there's no reason for him to come back, then. Wheeler, listening, is unimpressed.

Don and Gretchen go to an abandoned pier to meet Vikan; it's a satellite dead zone. T-Bag calls, asking what to do about Ralph. Don says it doesn't matter if he's Company or a Bible salesman; kill him. T-Bag prepares to pull the trigger, but hesitates. Rita urges him not to do it. If he does, Cole Pfeiffer — the good man he wanted to be — will be gone forever. T-Bag reels... and when Ralph is able to complete a Bible quotation that T-Bag's daddy used to recite to him, he lowers his gun and tells Rita to leave with Emily. He gives her all his money… and all of Ralph's money as well. After they leave, T-Bag unties Ralph... who knocks him out. He's Company after all.

The Doctor and Gen. Krantz go over Michael's CAT scan. The Doctor's has only ever seen a tumor of this sort so advanced once before. Suddenly Ferguson arrives, bearing Linc, who has come in the front door demanding to see his brother. He tells Krantz that this started with him, and it'll end with him; let Michael go. Krantz tells him he made the right decision, and takes him to see Michael. Vikan arrives at the pier; as he confirms that Scylla is complete, and the buyer's on the way with the money, Don suddenly shoots him and his bodyguard dead: no way was he giving Vikan thirty percent of the transaction. Gretchen demands to speak to Emily again; they call, but there’s no answer; we see a bound and gagged T-Bag led away by Ralph. Gretchen tells Don he's not leaving here until she knows that Emily's alive.

Lang says she's convinced Wheeler to let Mahone speak to the Attorney General. He gets in the car, expecting to be on the way to Dulles… but it's a perpetrator transport. Lang begins crying; Mahone's being arrested. Krantz tells Linc that if he gets them Scylla, he'll give Michael the best medical treatment in the world. As further incentive, Linc is shown a mysterious folder entitled "Tombstone II." Linc, staring at his unconscious and gravely ill brother, is left alone to contemplate his options.