

Steadman killed himself, the President stepped down, Lincoln was pardoned, and Kellerman seemingly committed suicide. Terrence Steadman (Jeff Perry) in ''John Doe'' We even learned of an embarrassing connection between the President and her brother Thomas Steadman. We learned of Scofield's father's involvement with the Company, Mahone's connection to Kim, and were introduced to the "Pad Man". The main storyline revolving around the conspiracy of The Company was neatly wrapped up by the end of the season. The storyline with Bellick and Sucre seemed a bit illogical and put together only for the sake of convenience. The chase for Westmoreland's five million dollar stash felt too much like a bad parody of an episode of The Amazing Race, and T-Bag's murderous journey felt like it dragged too long and too much of it felt a little too far fetched, even for a TV show. Not every story arc this season proved to be successful however. Lincoln managed to rescue his son and ultimately get a full pardon for his crimes by the end of the season. Scofield was prone to making a lot of emotional mistakes, mostly related to trying to help Sara Tancredi. Lincoln started asserting himself more, and actually felt like the more level-headed brother.

The main characters went through several transformations during the season as well. Kim was ruthless and unlike Mahone, had absolutely no redeeming qualities. No longer able to speak directly to President Reynolds, he instead was forced to take orders from the sinister, ever-smiling Agent Kim. Kellerman went through quite the evolution himself, mostly due to his failure to deliver on his duties given to him by the Company. Mahone (William Fitchner) in the season two finale, ''Sona'' In addition, Lincoln's girlfriend Veronica was also killed off in the premiere by the Company hit-man, Paul Kellerman. By the end of the season, several key characters were killed off by Mahone, including Tweener, Abruzzi, and Haywire. At first it seemed like cast members would drop like flies.

In another unprecedented move by the show's writers, this season featured a lot of deaths.

Mahone was given a mandate to eliminate every single Fox River escapee, and he did so meticulously, until his own demons started to catch up with him. Fichtner did a fantastic job in bringing this multi-dimensional character to life, and the troubled Mahone became one of the most compelling reasons to watch Prison Break this season. At times he'd scare you, and other moments you'd feel really sorry for him. Mahone proved to be the kind of character you loved to hate. The season started off with the convicts on the run, taking their own separate journeys, and introduced an intriguing new character that was meant to counter Michael Scofield's genius, federal agent Alexander Mahone, who was portrayed by character actor William Fichtner.
