Sara meets Linc in the Company's War Room, and is horrified to find that Linc has given Michael over to the care of Company doctors. Gen. Krantz claims to be acting out of empathy; she and Linc are guests during the surgery. Sara is at Michael's side as preparation for the surgery begins; he's dazed, but must remain awake throughout the process. Linc, in order to find out where Don and Gretchen are meeting the buyer, begins pulling T-Bag's teeth out. T-Bag gives up the location. As Mahone is transported incarceration, he insists on stopping to relieve himself. Wheeler is mistrustful, and only gives him fifteen seconds. Mahone reappears in short order… but he's taken a piece of pipe from the sink. Once they're back on the road he uses to shatter the car window, open the door from the outside, and escape. Wheeler and Lang give chase. Lang catches up with him first. Though she says she'll shoot, she ultimately allows him to get away, telling Wheeler that she lost him.

Linc recruits Sucre's help to go after Don and Gretchen, lying to him that the Company is trying to get the location of Scylla from Michael (so they have to get Scylla before the Company does). Michael's brain surgery begins, and Sara is discomfited to learn that the Company doctors are using an "advanced" technique unknown to her. Needles are inserted into his head to stimulate the hearing and memory portions of his cortex. It'll be the equivalent of a near-death experience, when your life flashes before your eyes. Michael hallucinates that he's back in his old cell at Fox River… and gets a visit from Charles Westmoreland, who assures Michael that his efforts haven't been for nothing. The answers are within him; he just hasn't found them yet.

Don and Gretchen wait for the buyer, but he hasn't arrived. Vikan's PDA is busted; but the contact number for the buyer, a Miami number, is still visible on screen. Don keeps it to himself. Gretchen's sister Rita calls, and tells her it'd be best if she stayed away from her and Emily. Gretchen also learns that T-Bag is now in the hands of the Company, which means that the Company likely now knows the location of the exchange. Linc and Sucre arrive, but Don and Gretchen are gone. They find Vikan's blood, still fresh. Linc surreptitiously calls the Company's Operations line, and asks them to find and track Don and Gretchen's car. Sucre finds two smashed cell phones and Vikan's PDA. They are observed by a mysterious man, the Representative, who is on the phone to somebody. He says there's somebody here, but it's not the seller: What should he do?

Gen. Krantz tells Sara that the procedure they're using on Michael has been used once before, and the patient led a long and happy life. He also tells her that he knows what she thinks of the work the Company does, but not everything is as it seems. The Doctor says that the tumor is nestled up against Michael's hippocampus, the seat of memory. In Michael's head, as he deals with guilt for all the people who have died because of him, Westmoreland prods him about Scylla. Not everything is as it seems. As Don plans to re-establish contact with the buyer, and set a new location for the exchange, Gretchen wonders why Don is uninterested in what Scylla actually contains. Could it be that if he knew what it was, he might have second thoughts about who he's selling it to? The Company tells Linc that the Don and Gretchen were seen at a convenience store. They go to the store. The cashier claims not to have seen them until Linc gets rough. They bought a phone. The cashier gives Linc a copy of the receipt. Linc uses the cell phone's tracking number. He learns that the phone was used two minutes ago, two miles away, at an abandoned factory.

Sara's concern grows: it turns out the tumor has spread into the hippocampus. Removing it may affect Michael's memory, though the doctor assures her that most memories aren't needed by the conscious mind anyway; Michael will likely never realize that anything's missing. Michael begins to convulse; he remembers the Scylla cardholder meeting he eavesdropped on. They're talking about a "bargain." He recalls Krantz equating Scylla with "power." He sees a flash of a periodic table. Westmoreland tells Michael he's sorry, but it's time to go. Michael's heart rate flat-lines, but — as Sara in the waking world implores him not to give up — Michael insists to Westmoreland that it's not finished yet. Michael has an epiphany… and wakes up. The Representative meets Don and Gretchen at the factory. He doesn't have the $125 million in cash; it'll be wired to them once he verifies that he truly has Scylla. As Linc and Sucre pull up, Don looks at the computer monitor over the Representative's shoulder. There are folders marked "Nuclear," "Fossil Fuel," "Wind," "Solar," and "Bargain." This is no little black book, Don muses aloud. The Representative is about to shoot Don and Gretchen when Linc and Sucre burst in. In the confusion the Representative escapes with Scylla.

Sara breaks it to Michael that the Company carried out his surgery. Michael tells her his epiphany: Scylla is something good. "Bargain" stands for the elements “B”oron, “Ar”gon, “Ga”llium, and “In”dium. It's been theorized that if those elements could be combined in a solar cell, you could harness 100% of the sun's energy. Sara speculates that there could be other advanced information in Scylla as well, like the surgical techniques they used on Michael. Scylla is the future. Scylla is valuable, and sought after not by people who want to bring down the Company… but by people who want to become the Company. Sara wonders why the Company has kept these advances secret rather than profiting from them. Michael points out that they may be maximizing their profits by holding out and keeping costs up until the time is right. Sucre tells Linc that he's out. He can't do it any more. He wants to live his own life. He's moving on. Linc is sad, but understanding. If Linc and Michael ever get down below and open up that scuba shop, there'll be a job there for Sucre. The two hug, and Sucre leaves.

Back at Company HQ, as Don and Gretchen are patched up by Company doctors, Gen. Krantz orders him to team up with them to retrieve Scylla. Linc balks, but Krantz tells him he's a Company employee now. He can't do this on his own. Besides, he might grow to like it at the Company: "Stranger things have happened – they certainly did in your family." Linc meets with Michael, and breaks it to him that he made a deal with the Company to save Michael’s life. Michael's not getting out of here just yet. Linc no longer cares about taking down the Company; he only wants to protect his family. Michael protests, but Linc gives him the "Tombstone II" folder that the General gave him earlier. Before their mother died, she worked for the Company too; Linc's just going into the family business