* AlasPoorScrappy: Sure, [[FaceHeelTurn he betrayed the protagonists]] and was an annoying, sarcastic punk who loved to run his mouth, but the way [[spoiler:Roland's]] death was executed in the show is pathetic enough for you to pity the man.
* AssPull: It's hard to imagine the [[spoiler: returns of Sara and Kellerman after they were both presumed dead]] were well thought out in advance. Also is that [[spoiler: 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 [[DeusExMachina comes up with a contrived way to resolve everything]] at the end of the series with no foreshadowing; Michael and Lincoln not actually being biologically related]], the list goes on.
* CompleteMonster:
** [[ScaryBlackMan Wyatt Mathewson]] from season 4 is a [[ProfessionalKiller professional hitman]] working for [[TheSyndicate the Company]] under its leader [[BigBad General Jonathan Krantz]]. He's the worst and most chilling PsychoForHire the Company has to offer, with nearly every scene involving him killing someone or [[ColdBloodedTorture torturing people to death]] while talking to them in a [[DissonantSerenity calm, soothing tone]]. He kills or tortures many people (mainly, anybody working against Krantz); this includes [[WouldHitAGirl women]] and even [[WouldHurtAChild murdering Cameron Mahone]] and [[BoomHeadshot 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 the SixthRangerTraitor Roland, he [[FalseReassurance 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.
** [[EvilMatriarch Christina Rose Scofield]], who first appears in season 4 but is mentioned earlier, is a high-ranking leader of the Company and [[BigBadDuumvirate along with General Krantz]] is revealed to [[TheManBehindTheMan have been behind most of the events in the show]]. She's a [[TheSociopath sociopathic]] {{insufferable genius}} who [[ItsAllAboutMe only cares about her own advancement]]. She sacrifices her whole family; [[ParentalAbandonment she abandoned both her sons Lincoln and Michael]] while they were kids without saying a word, rejected her husband after [[DefectorFromDecadence he turned on the Company]] and had him hunted down, and arranged for her adopted son Lincoln (whom she despised for his relative lack of intelligence) to be [[FrameUp framed]] and executed for a staged political assassination of Terence Steadman. She tries to [[EnemyCivilWar kill General Krantz]] to steal a device called "Scylla" and sell it for its [[{{Greed}} profitable military use]], then kills her conspirator [[YouHaveFailedMe 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 [[WarForFunAndProfit 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 [[HostageForMacGuffin 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.
* EnsembleDarkhorse:
** 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.
** Also Sucre and Mahone.
* FoeYay:
** Canonical, if unidirectional. T-Bag has had "designs" on Michael since their first meeting. It's not subtle. His nickname for Michael is 'Pretty'.
** Gretchen and Sofia. Gretchen continuously comments on how pretty Sofia is and seems to have NoSenseOfPersonalSpace with her. Also, there is Gretchen and Sara.
** And Gretchen and Linc is canonical, if also one-sided. There are two points when Gretchen wants to have sex with Linc and tells him so.
* GodModeSue: Michael Scofield. No plan will work without his involvement. He starts to become entirely precognizant in season 4.
* HarsherInHindsight: 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).
* HoYay: T-Bag and ''everyone'', especially Michael, but it's completely one-sided on his part.
* IdiotPlot: As strange as it sounds, arguably [[RefugeInAudacity part of its appeal]]. Viewer warning: disengage your WillingSuspensionOfDisbelief to effectively appreciate this series.
* JerkassWoobie: T-Bag is an almost perfect definition of this.
* LesYay: Gretchen with any adult female character she interacts with. Just watch "The Final Break".
* MagnificentBastard: Kellerman, T-Bag, the General.
* TheProblemWithLicensedGames: Reviews suggest that the game ''Prison Break: The Conspiracy'' is not so good.
* RescuedFromTheScrappyHeap: Bellick in Season 4. He TookALevelInKindness, helped the protagonists, saved Lincoln from getting killed, and even redeemed himself by [[spoiler:sacrificing his life so the team could acquire Scylla]].
* TheScrappy:
** Bellick in Season 2, when his SmugSnake nature was finally revealed. It got even worse in Season 3 when he was reduced to a whiny, cowardly inmate in Sona.
** Almost every character introduced in Season 3. At best, Gretchen and Whistler are [[BaseBreaker Base Breakers]].
** Roland, a sarcastic, stuck-up computer hacker [[{{Narcissist}} who thinks he's better and smarter than everyone else]].
** Michael is considered a CreatorsPet by some, especially in Season 4 when he became a GodModeSue.
** After his FaceHeelTurn, [[spoiler:Don Self]] became a very {{egregious}} SmugSnake who wasn't liked by ''anyone''. [[spoiler:Killing Miriam Hultz]] didn't help his case either.
* SeasonalRot: Seasons 3 and 4. The latter is more of a BrokenBase.
* ShockingSwerve: Near the end of the series, we find out that [[spoiler:Lincoln isn't Michael's biological brother]]. Since no one (Michael included) seemed to care, and since this was revealed at the last second, [[AssPull it's pretty obvious that this reveal was pulled out of the writers' asses]].
* {{Squick}}:
** [[spoiler: Caroline Reynolds and Terrance Steadman's [[BrotherSisterIncest incestuous relationship]], and the General and Gretchen's relationship]]).
** After having his hand cut off by Abruzzi, T-Bag forces a veterinarian (at knife point) to reattach it, and goes half a season before he has to abandon his hand. [[RunningGag The terrible condition of his hand is commented upon by various characters]].
** Everything T-Bag does falls under this.
* TheWoobie: '''Many''' of the characters.
** 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.
** Sucre is always the sweetest of the lot, going though ridiculous amounts of trouble for Michael and his [[YankTheDogsChain attempts to be reunited with his girlfriend Maricruz and his daughter are constantly thwarted]].
** Bellick: He starts off as an egotistical SmugSnake and a {{Jerkass}} who isn't above doing petty things to the prisoners when he doesn't get his way. But after an elaborate HumiliationConga, and the reveal that he [[spoiler: [[MamasBoy still lives with his mother]] and [[EvenBadMenLoveTheirMamas 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. [[spoiler: [[RedemptionEqualsDeath Dying to ultimately save]] and help the team at the end helped too.]]
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