* AbortedArc: While not quite aborted completely, many of the plans for Season 2 had to be altered when Patricia Wettig's minor role on ''Series/BrothersAndSisters'' turned into a regular when that show became a surprise hit. Instead of having a prominent role through the season, Reynolds was instead moved to being busy as President and also added on how she was really a pawn of the Company rather than the mastermind she'd appeared to be. It did end up altering the Kellerman plotline as instead of being at her side as her bodyguard, Kellerman was cut out of the loop, realizing Reynolds never cared for him and the realization she was just a pawn would push him to aid the brothers.
* 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 {{frame|Up}}d 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.
* 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.
** Female example: Gretchen with any adult female character she interacts with. Just watch "The Final Break".
* 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.
* 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 {{Base Breaking Character}}s.
** 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.
** 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.]]
* UnintentionallyUnsympathetic: It can be a tall order to feel sympathy for Mahone after the death of his child considering all the people he killed back in Season 2.
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