Episode 1: Scylla
Air Date: Sep 1, 2008
Michael uncovers unbelievable news in Los Angeles when he seeks revenge against Whistler and Gretchen for Sara, 's death. Michael and Lincoln are reunited with the gang and receive an offer from a Homeland Security Agent they cannot refuse. Mahone suffers a devastating loss, and T-Bag is deserted during his flight to freedom.
Episode 2: Breaking And Entering
Air Date: Sep 1, 2008
Michael, Lincoln and the others get a new team member, Roland, and work to copy the data card. Wyatt continues his quest to find the brothers. T-Bag makes his way north.
Episode 3: Shut Down
Air Date: Sep 8, 2008
Michael and the team have one day to find the next cardholder or they risk going back to prison. Mahone seeks revenge on Wyatt who is attempting to extract info on Sara, 's whereabouts, while T-Bag finds the gateway to his new identity and future.
Episode 4: Eagles And Angels
Air Date: Sep 15, 2008
Michael, Lincoln and Sucre must crash a police benefit to obtain the next card key. Reeling from another death, Sarah falls back into an old habit. T-Bag arouses suspicion and runs into some old , friends, his first day on the job.
Episode 5: Safe And Sound
Air Date: Sep 22, 2008
Michael and Lincoln make their way to the Treasury Department in search of the next key card holder; an awkward alliance formed by T-Bag at his new job arouses the suspicions of Sucre and Bellick; Wyatt uses his magic touch on Gretchen.
Episode 6: Blow Out
Air Date: Sep 29, 2008
Michael and the team tracks a key card holder to a racetrack; Mahone gets caught with something priceless; Wyatt targets Agent Self; T-Bag starts to figure out Whistler's code.
Episode 7: Five The Hard Way
Air Date: Oct 6, 2008
Lincoln takes members of the team to Las Vegas where Sucre gets an indecent proposal. Sarah learns about Michaela 's condition, and Roland pushes his luck too far. Gretchen teams up with T-Bag who makes an offer to Michael he cannot refuse.
Meanwhile, the secrets in Whistlera 's bird book are finally revealed.
Episode 8: The Price
Air Date: Oct 20, 2008
Lincoln works to retrieve the final card, which is being held by the General.
Michael and Self are forced to work with Gretchen. Meanwhile, Roland continues to be berated for losing the transcribing device in Las Vegas
Episode 9: Greatness Achieved
Air Date: Nov 3, 2008
Wyatt gets a taste of his own medicine, and Mahone finds some resolution. T-Bag scrambles when the police investigate his missing co-worker while Gretchen gets cozy with a Company man.
Michael's condition continues to worsen, and a team member makes the ultimate sacrifice while planning the underground break-in for Scylla.
Episode 10: The Legend
Air Date: Nov 10, 2008
Sara is left with no choice but to take Michael to the hospital as his condtion rapidly worsens.
Sucre and Lincoln are faced with unknown territory as they are left in charge of the operation.
Agent Self makes a surprising ally
Episode 11: Quiet Riot
Air Date: Nov 17, 2008
Michael risks his life by breaking into the Company headquarters with Sucre's help. Gretchen tries to get the last card key with a meeting with the general.
Episode 12: Selfless
Air Date: Nov 24, 2008
As the search for Scylla comes to a surprising end, Sarah takes a hostage, T-Bag and Gretchen have their last stand at Gate, and Michael and Lincoln are betrayed by one of their own as they finally get to go face-to-face with the General.
Episode 13: Deal Or No Deal
Air Date: Dec 1, 2008
It's up to Michael to hold the gang together after they find out they were betrayed by one of their own. Meanwhile, Gretchen is blackmailed by T-Bag's new partner.
Episode 14: Just Business
Air Date: Dec 8, 2008
Michael and Lincoln work to get Scylla back from Gretchen and her new partner. Meanwhile, Mahone meets up with an old colleague, and T-Bag is put to the test.
Episode 15: Going Under
Air Date: Dec 15, 2008
Michael recieves medical attention. Charles Westmoreland helps uncover the real secrets of Scylla. Lincoln and Sucre do everything in their power to retrieve Scylla before it's gone forever.
Episode 16: The Sunshine State
Air Date: Dec 22, 2008
Lincoln and his new partners arrive in Miami to recover Scylla from its shocking new owner, and Sara searches for a missing Michael who learns some surprising information about his past. Meanwhile, a double-crossing leads to a death and an arrest in The Sunshine State.
Episode 17: The Mother Lode
Air Date: Apr 17, 2009
Michael and Sara journey to Miami while Lincoln meets with his mother.
T-Bag and Self's mission to locate Scylla takes a dramatic turn.
The General comes under pressure.
Episode 18: Vs.
Air Date: Apr 24, 2009
Michael and Lincoln square-off over Scylla as Christina orders a kill shot and set sets her plan in motion. Sarah receives some unexpected news, T-Bag causes a scene at the Indian Embassy and Pad Man, 's paranoia leads to a death.
Episode 19: S.o.b.
Air Date: May 1, 2009
Michael has an uneasy reunion with Christina, who drops a bombshell regarding Lincoln. Lincoln races to stop Christina, 's deadly master plan. T-Bag must prove he is a Company man.
Episode 20: Cowboys And Indians
Air Date: May 8, 2009
Pandemonium erupts at the hotel following the assassination, and Christina puts the final pieces of her plan together. Meanwhile, the General makes good on his threat, and Michael is forced to choose between saving either Lincoln or Sara.
Episode 21: Rate Of Exchange
Air Date: May 15, 2009
Familiar faces return to help Michael end his quest to bring down The Company once and for all.
Episode 23: The Old Ball and Chain
Air Date: May 25, 2009
Sara is imprisoned after the murder. She was sent to women's prison by government and she spend her 25 years of life there. She is fearful for her future as she was pregnant and she has to create a bond with her enemies in order to cope up with the environment. Her condition in jail made Michael to take some action.