Linc — at a hotel with Don, T-Bag, and Gretchen — calls Sara, and tells her he's in Florida trying to get Scylla back for the Company. Sara doesn't think the Company will really let them live even if he succeeds, but Linc says he doesn't have a choice. The Company's data tech has traced the Representative's cell phone to a local nightclub. Linc goes to the club. The bartender Brent won't help; but the cocktail waitress, Tia, seems to know something. When Linc approaches her, Brent attacks him, but Linc makes short work of him. Tia says the man they're looking for dates another waitress there, Erica. Linc tells Tia to take him to her; however, she sets him up: Linc is ambushed, and shot at. Linc is unharmed, but in the melee Tia gets away, and jumps in a car with the shooter... and the Representative. Linc has gotten a hold of her wallet. He returns to the hotel, and tells Don and T-Bag to search her apartment for information.

Michael awakens in new surroundings: a cabin in a secluded, wooded area. Michael learns that he's sixty miles from civilization, and the woods are full of mountain lions. Also there is a Dr. Ferguson, a psychiatrist assigned by General Krantz to talk to Michael. He tells Michael his mother is still alive… and working for the Company. She left Michael and Linc to protect them. Michael asks about Linc going to the electric chair; Knowlton says that their mother was deep in a rainforest in Madagascar at the time, without any communication with the outside world. When she found out about it, it was far too late for her to stop the plan the Company had for the Burrows brothers. Michael isn't buying this, and asks to speak to her on the phone. Knowlton says not until he's ready to join her… working for the Company. He could work with her on the Scylla project. To try to prove his claims, Knowlton has a photo album full of pictures from Michael's childhood. He begins to play on Michael’s longing for his family and childhood. Michael's still not buying, but he's shaken. Later Krantz calls Knowlton to check on his progress. Knowlton thinks he can turn Michael in three days. Krantz wants him to speed up the process with pentothal; Knowlton protests that it'd be tantamount to a lobotomy. Besides, if Michael decides to turn on his own, it'll be his decision and reasoning: the Company will own him forever. Krantz backs down, but threatens Knowlton with a lobotomy if it turns out that Michael's playing him.

Sara meets with Krantz; she wants to help with Michael's recovery. Krantz refuses, telling her she'll be reunited with Michael in just a few days. He tells her the future for them looks good. Michael will be using his talents on a global scale, and so will she. Sara becomes apprehensive, and demands to know what he's doing to Michael. "Putting an end to this exhausting game of cat and mouse," sighs Krantz. Later Sara is paged to a mysterious meeting in MacArthur Park. A payphone rings. She runs to answer it, and is suddenly snatched off the street by two masked men, who throw a hood over her head and toss her in a van. The abductor is Lisa Tabak, who simply wanted to talk to Sara without the Company knowing. She gives Sara Michael's location, and warns her that they're "carving out his personality" to recruit him.

Back at the Miami hotel, Gretchen is concerned: she can't find out anything about the buyer, and people who can't be found are generally Company. She then unexpectedly comes on to Linc, but just at that moment T-Bag and Don return from searching Tia's apartment. They've found nothing, and say that they've decided that Linc is no longer in charge; Don is. At that moment Mahone enters, tipping the scales of power back in Linc's favor. Tia's credit card is traced to a gift shop at the marina. Could the Representative be trying to smuggle Scylla out of the country by boat? Don and Mahone ask the Harbor Master, Stember, if he recognizes a photo of Tia. When he won't help, Don flashes his old Homeland Security badge, and claims to be investigating the smuggling of contraband Cuban cigars. Stember folds, and tells them she was there with a guy who asked if he could move a private charter to a berth further down the dock; further away, Mahone realizes, from the Coast Guard slip. Said charter has just arrived. Linc, T-Bag, Gretchen, and Don do a spot luggage check on the passengers, looking for Scylla. One guy in sunglasses with a Scylla-sized backpack bolts. Mahone and Linc give chase, but the guy's just panicking because he's got three marijuana joints on him, and he's on probation. This isn't their guy. Mahone and Don go back to Stember, and demand a copy of yesterday's security tape. They return to the hotel. T-Bag speculates that maybe the buyer was on the boat coming in. Self points out that they wouldn't have been traveling under their real name, so getting a passenger manifest won't help. Meanwhile, Linc levels with Mahone that he's working with the Company to get all of them off the hook: Pam, LJ, everybody. Mahone cautiously allows that this is the first time they've ever had the opportunity to have any genuine leverage against the Company... but they don't have Scylla yet. Gretchen, who has been searching through mug shots on her computer, finds the Representative's photo. His real name is Scott Carruth, but she keeps the information to herself. By the time Don finds his image on the security tape, Gretchen is gone… to take a secret meeting with Carruth. They know each other from the Company. She offers to work for him, for the right price. He offers $10 million.

Michael compares old photos of his mother with what Knowlton says are recent photos of her in Argentina. There's also a handwritten note, and Michael recognizes the handwriting as hers. Sara, on her way to rescue Michael, calls Linc to tell him what's going on. T-Bag overhears, and calls Krantz to warn him. Krantz, angry, realizes what must have happened. He takes a photo of himself and Lisa, and throws it in the trash. He then calls Knowlton, and tells him to administer the drug and damn the consequences; Michael needs to be pliable and ready for transport in twenty minutes. If Michael dies, c'est la vie. Ferguson restrains Michael, but a loud noise from the bathroom distracts him. Michael has rigged the water heater to explode. In the fracas Michael gets free of Ferguson's grip, and gets a hold of his gun. He forces Ferguson to inject Knowlton with the pentothal, and then handcuff himself to a bedpost. He then flees the cabin. Company agents arrive in short order, and free Ferguson. Michael is nearly caught, the Company SUV bearing down on him; but then the SUV is rammed by another car... driven by Sara. Michael jumps in her car, and the two speed away.

Gretchen returns to the others, and tells them she's found the buyer. She lures them to the parking lot of the high rise where she claims he's staying. They're ambushed by Carruth and his goons, and Gretchen turns her gun on the gang. As Don curses her out for her apparent betrayal, Gretchen suddenly turns, and takes out Carruth's goons. Gretchen, thinking of her daughter Emily, tells Carruth that right now she wants her life back far more than she wants money. The others pull their guns; Carruth is surrounded, but he says that Scylla is already gone. He then suddenly whips out his gun, and shoots Gretchen in the side. Gretchen shoots him right between the eyes. As T-Bag goes through his pockets, a police siren is heard in the distance. They've got to run, but what'll they do about the wounded Gretchen? Don insists that Linc kill her; she can't be trusted. T-Bag, an unexpected voice of reason and compassion, dissents; after all, Gretchen has a kid who's only eight years old. Linc decides to leave her there for the police, warning her to keep her mouth shut. Gretchen says not to worry; she knows exactly what Krantz will do to her in prison if she talks.

Michael and Sara, having driven for an hour, take a rest by the side of the road. He's shaken, and hasn't spoken in all that time. He finally tells her that he thinks his mother is alive. Linc answers Carruth's purloined cell phone. He tells whoever is on the other end that Carruth is dead, and now he's coming after her. The woman on the other end hangs up. She's an elegant woman in a well-appointed mansion. Her aide asks who that was. She says it was her son… her son Lincoln