Plot summary
The brothers manage to find Whistler and arrange the exchange in a public place, which Scofield has designated, only to make certain that L.J. and Sofia are fine. Scofield arranges the real trade to be in a museum. Morgan is forced to remove her weapons to enter the museum. L.J. and Whistler are successfully exchanged. Sofia realizes that Whistler is a Company man and decides to go with Lincoln. Having predicted that Morgan has put an operative on every exit, Scofield triggers the alarm. They exit through the main door before a shootout ensues between the Company men and the police.
Scofield moves to kill Morgan, but his hesitation allows her to flee. Sofia is wounded and taken to a hospital. Meanwhile, Bagwell gets money from Lechero's concubine and proceeds to kill him. The inmates accept him as the new leader. Sucre doesn't break after a long torture and is sent inside Sona. Mahone joins Whistler's plan. Gallego and his father successfully pass the border and rejoin their family. Scofield decides to continue to search for and kill Morgan, starting with Whistler's apartment.
Credits
Adapted from Wikipedia contributors, Prison Break season 3. HTML formatting and reference markers removed.