Lincoln Burrows (Dominic Purcell) meets with General Krantz (Leon Russom) in his office and agrees to a deal: in exchange for Lincoln's help in retrieving Scylla, the Company will give Michael Scofield (Wentworth Miller) the life-saving operation he needs. With Sucre alongside, information tortured out of T-Bag (Robert Knepper) in hand, and the Company providing off-site support, Lincoln follows the trail of Donald Self (Michael Rapaport) and Gretchen Morgan (Jodi Lyn O'Keefe) across Los Angeles as they try to evade surveillance and meet with a buyer interested in Scylla. Lincoln and Sucre arrive just as the buyer betrays Morgan and Self, shooting the latter. The buyer escapes with Scylla while Gretchen and Self are caught. When they return to the Company's headquarters, Sucre takes his leave and promises to meet up with Michael and Lincoln again down the road. The General is angry that Lincoln let the buyer escape, and orders Lincoln to work with Gretchen, Self, and T-Bag to retrieve Scylla.
Alexander Mahone (William Fichtner) is being transported to federal custody by Agents Felicia Lang (Barbara Eve Harris) and Mark Wheeler (Jason Davis). Using his knowledge of FBI regulations, Mahone forces Wheeler to let him stop at a restroom, and while there he steals a pipe. Later, during the drive, Mahone uses the pipe to escape the moving FBI sedan and flees into the woods on foot. Lang is able to catch up with him and threatens to shoot, but he calls her bluff and walks away. Lang shoots, but purposely misses. When Wheeler arrives, Lang lies about which direction Mahone fled.
While Sara (Sarah Wayne Callies) watches, the Company surgeons operate on Michael using a surgery technique that she has never seen before. While under the effects of anaesthesia, Michael dreams of being back in his cell at Fox River, where his wall is covered in photos and documents about the events of the series. He also sees a vision of Charles Westmoreland (Muse Watson), who gives him cryptic clues about Scylla and the Company. Phrases overheard while spying on the General and the cardholders, particularly the word "bargain," keep popping out at him, but he has only just seen these clues when his heart begins to flatline, and it's only his memories of Sara and her words that seem to snap him back to reality. Once he's awake, Michael is able to put together the clues and tell Sara what he's realized: Scylla is not a record of Company agents and operations, but instead a database of the most cutting-edge scientific knowledge in the world. The word "bargain" referred to the chemical elements "Boron" (B), "Argon" (Ar), "Gallium" (Ga) and "Indium" (In), which would be combined as part of a revolutionary solar power technology. Michael claims that the kind of knowledge Scylla contains would be vital to scientific and cultural development, and with it, the Company has leverage over the rest of the Western world. People want Scylla not to destroy the Company, but to become the Company.
When Lincoln returns, Michael tries to impart what he's learned but Lincoln doesn't care. He isn't concerned with stopping the Company, only with protecting his family, likening his deal with the Company to Michael's original plan to break out of Fox River. He also shares another revelation, one learned from the General's files: Michael and Lincoln's mother also worked for the Company. Michael pleads with Lincoln not to help their enemy, but Lincoln, satisfied that this action will keep his brother safe, leaves Michael in his hospital room to rejoin the hunt for Scylla.
- "It’s difficult to remember a show which stumbled so badly in the middle of a season."
- ―The TV Critic's Review