Alas, Poor Scrappy: Sure, he betrayed the protagonists and was an annoying, sarcastic punk who loved to run his mouth, but the way Roland's death was executed in the show is pathetic enough for you to pity the man.
Alternate Character Interpretation: During his time as Michael's cellmate, Haywire expresses no interest in escaping when Michael asks if he has ever considered it, telling Michael that he should report to Bellick if he knows anyone having such plans. In all his later appearances, he does want to escape, first trying to do it alone before managing to force the rest of the Fox River Eight to take him with them. Did Haywire have a genuine change of heart about wanting to escape, or did he always want to escape and was initially just pretending to be trusted enough to remain in the general prison population? Given that he was pretending to be on medication…
Arc Fatigue: Though the season was reduced to thirteen episodes, the third season was criticized by some for trying to repeat the magic of the first season but failing to fully replicate the tension or excitement, and instead felt longer than the first season's full slate of episodes.
Ass Pull: It's hard to imagine the returns of Sara and Kellerman after they were both presumed dead were well thought out in advance. Also is that the fourth season opening shows us that the Sona prisoners escaped; C-Note's happy ending in season 2 is ignored; the company's very public reveal in season 2 has been ignored; Lincoln is revealed to have been a killer in his backstory - when it was repeatedly established that his character was incapable of doing so; Kellerman comes up with a contrived way to resolve everything at the end of the series with no foreshadowing; Michael and Lincoln supposedly not being biologically related, the list goes on.
Sara's death in general as most found it hard to believe that the kidnappers would be so shortsighted as to immediately kill the love of Michael's life (as he had barely begun breaking Whistler out at this point) after Lincoln tries to intervene as a warning and threat instead of just cutting off body parts, as they threaten to do to LJ just moments after telling Lincoln this. There had to have been a more logical way to kill the character off.
Near the end of series four, Christina claims that Michael and Lincoln aren't even brothers. Neither of them cares, it's not even brought up again, and the writer of that episode revealed on the audio commentary that Christina was lying.
Better on DVD: The Season 4 DVD features “The Final Break” TV movie that serves as an epilogue to the original four season run.
Christina Rose Scofield, who first appears in season 4 but is mentioned earlier, is a high-ranking leader of the Company and along with General Krantz is revealed to have been behind most of the events in the show. A sociopath who only cares about her own advancement, she sacrifices her whole family: She abandoned both her sons Lincoln and Michael while they were kids without saying a word; rejected her husband after he turned on the Company and had him hunted down; and arranged for Lincoln (whom she despised for his relative lack of intelligence) to be framed and executed for a staged political assassination of Terence Steadman. She tries to kill General Krantz to steal a device called "Scylla" and sell it for its profitable military use, then kills her conspirator when he botches the hit. She pretends to sell the technology to a renowned Indian scientist/politician, but instead has him assassinated in public and frames Lincoln again, along with Michael, Mahone and Don Self. Christina intends to unleash a decades-long war between India and China so she can sell the tech to both sides for a quick profit, knowing that it would quickly escalate into a global conflict. When Michael steals Scylla back from her, she kidnaps Lincoln and gives Michael an ultimatum for its return by shooting Lincoln in the lung to watch him die slowly. She later tries to kill Michael when he's ruined her plans one too many times.
Jacob Anton Ness is a noted economics professor from the University of Ithaca who is also known as Poseidon, a narcissistic deep-cover CIA agent who serves as the Big Bad of the 2017 revival. Revealed to be The Man Behind the Man of the Direct to Video movie The Final Break, he tries to press Michael Scofield into faking his death and joining his rogue cell 21 Void by threatening to imprison Michael's family and friends for life without parole. When Michael initially refuses, Jacob has Michael's pregnant wife Sara Scofield incarcerated for Christina Scofield's death. After Michael is forced to fake his death, Jacob enslaves him into breaking out terrorists and rogue agents—including the head of Yemen's ISIS—who act against America's interests. Knowing Michael would eventually betray him, Jacob kills CIA Deputy Chief Harlan Gaines and frames Michael for Gaines's death before he leaves him to die in Yemen's Ogygia prison. Over the next four years, he erases Michael's identity and marries his wife. During this time he proceeds to gaslight her into believing Michael is dead, going as far as framing Kellerman for hacking her phone after he has him killed and hiring his henchmen A&W and Van Gogh to terrorize her and Michael's son Mike before having the henchmen imprisoned to prove Jacob's "innocence." When she finds out Jacob is indeed Poseidon, he kidnaps Mike and Sara and tricks Mike into teaching him how to draw maps in the shapes of child-like drawings, all while planning to have Michael and Sara trapped and killed in a vacation home. When they escape the home, Jacob abducts Mike and brainwashes him into believing that Sara died in the house and that Michael is a terrorist named Kaniel Outis.
Season 4: Wyatt Mathewson is a hitman working for the Company under its leader General Jonathan Krantz. He's the worst and most chilling assassin the Company has to offer, with nearly every scene involving him killing someone or torturing people to death while talking to them in a calm, soothing tone. He kills or tortures many people (mainly, anybody working against Krantz); this includes women and even murdering Cameron Mahone and blowing the child's head off post-mortem to mutilate the corpse just to spite his father Alexander Mahone further. When he's given intel on Scofield and his crew by Roland, he promises to give Roland $1 million and to let him go in exchange for the others. Once there, Wyatt progressively shoots Roland in the kneecap, then his thigh, and then in his stomach to watch him bleed out.
T-Bag. He was originally a guest star only slated to appear in two episodes but quickly became the most popular character on the show. The show repeatedly demonstrated his Hidden Depths, showing him to be a far more intelligent and resourceful character than the one-dimensional bad guy he initially appeared to be, giving him some Evil Is Cool appeal.
Mahone has quite a large fanbase, enough for fans to be disappointed that he wouldn't be returning for season five due to the actor's prior commitments.
Sucre, for his unflagging loyalty and sweet demeanor. When he wasn't featured in the first trailer for season 5, many took immediately to comment sections demanding to know where he was.
Harsher in Hindsight: Tweener's actor Lane Garrison went to prison for real after killing a girl while drunk driving shortly after finishing filming his role on the show (the timing was so tight that he was still appearing on the show for a couple months after going behind bars).
Ho Yay: T-Bag and everyone, especially Michael, but it's completely one-sided on his part.
Female example: Gretchen with any adult female character she interacts with. Just watch "The Final Break".
There's a fair amount between Michael and Mahone with the pair constantly giving each other deeply intense and lingering looks right from their very first meeting. At one point in Season 3, while Mahone is threatening Michael against leaving him behind in Sona, he pins Michael up against the wall, gets right into his personal space and even spends a majority of the encounter whispering directly into Michael's ear.
Jerkass Woobie: T-Bag is an almost perfect definition of this.
Moral Event Horizon: Poseidon (aka Jacob Ness) from Season 5 is a psychopath who will stop at nothing to get what he wants. As a result, it's not a question of if Poseidon has crossed the MEH, but when. Here are a few milestones:
The Reveal that he had Sara incarcerated for the murder of Christina Scofield when Michael initially refused his loaded offer. This act makes him directly responsible for the torment Sara suffers in The Final Break and makes his marriage to her even more sickening in hindsight.
The fact that he allied himself with ISIL. While it's one thing to want to change foreign affairs, it's another to willingly support a death cult looking to impose a brutal caliphate on Yemen's population.
Just when you think Poseidon wasn't bad enough, the finale has him brainwashing Mike into believing that his father is dead and that Micahel is a terrorist imposter. Hearing a brainwashed Mike scream at his father to stay away from him on phone was a heartbreaking scene, and one that made many fans scream for Jacob's blood.
Narm: Callies refused to return for season three just to be killed off and it's extremely obvious a body double is being used for Sara in her scenes (not to mention the head in the box really doesn't look anything like her), making them somewhat hard to take seriously and distracting.
Rescued from the Scrappy Heap: Bellick in Season 4. He Took a Level in Kindness, helped the protagonists, saved Lincoln from getting killed, and even redeemed himself by sacrificing his life so the team could acquire Scylla.
Bellick in Season 2, when his Smug Snake nature was finally revealed. It got even worse in Season 3 when he was reduced to a whiny, cowardly inmate in Sona.
They Wasted a Perfectly Good Character: While the show runners said that Veronica was killed simply because they ran out of ideas for her storyline, after being such a dynamic presence in season 1 Veronica deserved better, even if it would have just meant spending a good chunk of time as a hostage to The Conspiracy.
Alex Mahone, who is a brilliant detective, but is manipulated by forces beyond his control, is addicted to his medication and then loses his young son.
Michael: he's a good decent guy who suffers ridiculous levels of abuse for doing the right things.
Bellick: He starts off as an egotistical Smug Snake and a Jerkass who isn't above doing petty things to the prisoners when he doesn't get his way. But after an elaborate Humiliation Conga, and the reveal that he still lives with his mother and cares deeply about her, and goes to such lengths as to write a note for her for Sucre to pass on have made him far more sympathetic. Dying to ultimately save and help the team at the end helped too.
While many fans hate Roland for being a narcissist computer hacker who ends up betraying the team, some fans actually feel sorry for him. Most of the group already seemed to hate Roland from the start, with Lincoln calling him douche the minute they met. Roland was constantly bullied by the team, especially by Lincoln just for opening his mouth. Roland was also very important to the team because of his hacking skills as they wouldn't have gotten the Scylla keys without them. While Roland's betrayal was wrong, some viewers felt the team pushed Roland too far. Not only that, his death at the hands of Wyatt was horrible.
Mahone barely subverts this. It can be hard to feel sympathy for Mahone after the death of his child considering all the people he killed back in Season 2. But he goes through so much crap and punishment before the death of his son that you can't help but feel his suffered enough. Not to mention, he does feel remorse for much of his actions.
It can be even harder buying Kellerman's redemption after all the people he's killed in both Seasons 1 and 2. It's even harder to like him when you remember he taunted LJ with the deaths of his mother and step-father. Not to mention, he tortured many people including Sarah. And unlike Mahone, Kellerman was shown to have no remorse for any of his actions, until he failed for the last time.
Any possible redemption for Bellick in season 4 can be difficult to swallow, especially after some of the shit he pulled for the first few seasons.
