Michael is in Los Angeles to kill Gretchen and Whistler, while Linc, Sofia and LJ chill in Panama. SONA is burned down and Bellick, Sucre and T-bag escape.

After The Company attempts to kill all the main players, they re-unite under a new 'handler', Self (a Homeland Security agent), they go after the Company to attempt to bring down the shadow organization once and for all.

The Company continues to work on locating Michael, Linc and the team, while the brothers lead their

Michael attempts to track the cardholder and avoid going back to prison. Wyatt finds new information regarding Sara's whereabouts. T-Bag uses a new identity to make a new life for himself.

With a camera phone far off, the gang gets an image of a license plate which is traced to a Turkish consulate Erol Tabak. As they are staking the man, Roland's data tracking device reveals that the cardholder is not the consul. It's his wife, Lisa Tabak.

Sara realizes that she's being followed and ditches her pursuer. Mahone meets up with his ex-wife to get the positive ID on their son's killer. Michael and Linc lead Bellick and Sucre on a dual mission to both find T-bag and break-in to the office of another cardholder (who happens to be a big-wig at Treasury with his office in the Federal Building).

The crew executes a daring attempt at the data on that card in the Federal Building, while T-bag continues to muddle along trying to figure out what he's landed himself into.

Mahone, meanwhile, has begun an odyssey to track and eliminate his son's killer that the team has also figured out is the assassin that is after them all.

Bellick causes a disturbance at a betting window of a racetrack to distract security. This allows Michael and Mahone to sneak into the operations manager's office and tape the device to the man's desk. Roland picks up the signal. Cardholder four is Nathaneal Edison, who has bet on a horse named SparkleKid. lincoln does something to cause SparkleKid to get a late start from the gate. Edison is furious and goes to speak to the operations manager. With the card near the desk, Roland pulls all of the information off Edison's device.

Gretchen holds T-Bag hostage in his house and she cuts his arm with a knife. He reveals what little he knows about Scylla.