Michael Scofield (Wentworth Miller) has tracked Gretchen Morgan (Jodi Lyn O'Keefe) and James Whistler (Chris Vance) to Los Angeles.
Before he and Gretchen can finish their operation, Michael arrives, planning to kill them as revenge for the death of Sara Tancredi (Sarah Wayne Callies).
They discuss the recent events in Sona: the prisoners rioted, burning the place down and allowing Theodore "T-Bag" Bagwell (Robert Knepper), Fernando Sucre (Amaury Nolasco) and Brad Bellick (Wade Williams) to escape.
Fearing that something may have happened to Pam and Cameron, he quickly steps out of the car and runs towards the house, but the police officer stop him and tells him "that you don't want to go in there".
Unable to trust people within the government, Self arranges to have Michael and Lincoln be part of an unofficial, off-the-books operation to recover Scylla from the Company, with their freedom guaranteed when it's all over.
When Wyatt attacks the group at their supposedly secret hideout, Michael, Lincoln and Sara decide to join Self's team, believing that they can only be safe once the Company is destroyed.
He tries to get to San Diego, following direction written in Whistler's bird book (which, unbeknownst to him, contains information on where to decode Scylla), but his drivers steal T-Bag's money and abandon him in the desert with their overweight companion.