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  • Accidental Innuendo:
    • A lot of Lance's dialog comes off as unintentionally sexual because of all his rock puns. Season 2 Episode 1 had these lines by Lance and Kitty:
      Kitty: Shouldn't you be erupting somewhere?
      Lance: Hey Kitty, you wanna see some real shaking?
    • Scott's Badass Boast of "You want it raw? Then take it raw!" takes on another meaning when one factors in the fact that "taking it raw" is a colloquialism for unprotected sex.
  • Adorkable:
    • Kurt with his playful nature, adorable elf ears, and constant joking, as well as his tendency to make Sci-Fi references with Scott when the two are doing something.
      Scott: Teleporter to Maximum, Mr Wagner.
      Kurt: Aye Captain!
      Scott: ENGAGE! *Both teleport out of scene.*
    • Kitty Pryde has him trumped. Geeky, a little on the clumsy side, and just plain adorable, especially when she's dancing.
    • Rogue's shyness and social awkwardness makes her this.
    • Toad on his better days. He's awkward, not that smart and The Chew Toy. He also isn't very popular at school but his goofiness and his crush on Wanda make him lovable.
  • Alternative Character Interpretation:
    • The Brotherhood:
      • They're an Ineffectual Sympathetic Villain team, but does that mean they're bad people who are just too pathetic to be a serious threat, or are they actually misunderstood misfits who never got a chance?
      • By extension, it's shown that Xavier would gladly welcome them if they wanted to join, but did he try hard enough to reach out to them, or did he leave them to their own devices so as to not have to worry about the difficulties they'd bring?
      • Lance in particular: Did he really have a heroic side, or was he solely motivated by trying to get Kitty to like him? Can it be both in the end, with Lance starting to do good things just to get Kitty into liking him, but ultimately developed into a better man because of it? In this case, is it Love Redeems, or is Lance just turning Kitty into a prize for him to 'win' by being good?
    • Scott: Was he just trying to be a responsible though imperfect leader, or just a full-on Jerkass?
    • Were the New Recruits complete idiots who crossed into Too Dumb to Live, or just inexperienced and excited at the prospect of being mutants that they got ahead of themselves a few times? More specifically, did Bobby/Iceman truly learn his lesson and become a good asset to the X-Men/New Mutants, or were his Too Dumb to Live credential just swept under the rug?
    • Was Spyke an asshole who was Easily Forgiven only for being a newbie and Storm's relative, or just a budding anti-hero who was too young and constrained to do it right?
    • Was Mystique shape-shifting into Risty because she wanted to spend some time with Rogue or to manipulate her daughter into letting her access the X-mansion? Or was it a mix of both? The fact that she did not pursue a similar friendship with her own biological son strongly points to the second interpretation.
    • All of Magneto's actions with Wanda. Given how powerful Wanda is, her lack of control is indeed something to fear. Having Mastermind Mind Rape her could've been more of a last resort since he did try to resolve things the old fashioned way beforehand. Of course, then there's the question of how much he regretted the act.
  • Arc Fatigue: Season 2 has very few ongoing story arcs, and due to the fairly standalone nature, drags on without anything particularly interesting happening until the finale episodes, where mutants are outed to the world.
  • Angst? What Angst?: Forge. He was trapped in his own pocket-dimension for 20 years and the kid takes it surprisingly well. Even when mentioning finding his parents, he just jokingly says he's 20 years late for curfew.
  • Base-Breaking Character:
    • Avalanche. Due to Characterization Marches On, he went from being a volatile Jerkass with a Hair-Trigger Temper and a shade of Manipulative Bastard in his debut episode who nearly killed Kitty and her parents to spending season 2 as a love-sick, but hot-headed, Nice Guy chasing Kitty, and by the last season settles on being an Jerk with a Heart of Gold Anti-Villain. Some adored him as a result and found his relationship with Kitty to be sweet, while others thought it was forced and thought he came off as a creep (not helped by how some scenes indicated he didn't care for Kitty's consent).
    • Jean. To some extent there's a great degree of Vindicated by History; for years she was written off as an annoying Damsel Scrappy with a Holier Than Thou attitude, but a lot of this came from the Brotherhood and Scogue fans, and some of the things she was hated for were very much a case of Double Standard. Long after the fact though, many modern X-Men fans who adore Jean Grey cite this show's version as being one of their favorite takes on her.
    • Cyclops is similar; at-the-time and for some years after he was commonly bashed by Brotherhood fans but was liked by fans of Jean/Scott, Rogue/Scott, and the Kurt-Scott bromance the show created. In a weird way, both opinions became more extreme with age, as fans of the show gradually became more aware of the comics (if not jumping into the comic fandom as a whole), where he's a Base Breaking Character there as well, resulting in people using traits from the comic version to cement or justify their opinions of the Evolution version, even aspects that don't match his characterisation in the show.
    • The New Recruits, especially Iceman, got a lot of hate for their idiocy, while others enjoyed it and found them hilarious. "Joyride" is generally cited as an example of them going too far, though.
  • Best Known for the Fanservice:
    • "Spykecam", the episode where Sabretooth first appears, is better remembered for Rogue and Kitty's dance after Rogue absorbs a bit of her skills. While the show was always well-animated, this got an Animation Bump (and was modeled after a similar dance in Buffy the Vampire Slayer), making for some very smooth and sensual dance moves.
    • "Survival of the Fittest" had Jean Grey dressed as Lara Croft, essentially, with a sexy green tank top, shorts, and a single long braid the entire episode.
    • "Walk on the Wild Side" is remembered for the X-girls and Boom Boom donning sexy black leather outfits to fight crime.
  • Bizarro Episode:
    • "Walk On The Wild Side" comes off as an Anvilicious "feminism" episode that has just gotten worse with age. There's also the bizarre inclusion of a music video dance montage set to "Only A Girl", of which nothing similar will ever happen again in any episode. Since it's filler, people who dislike it tend to simply ignore its presence.
    • "African Storm", since the episode is about a shaman from Storm's tribe stealing her soul, when magic is only mentioned a handful of times throughout the entire series. Sadly, this is the only episode where Storm is the main focus.
    • An episode had Forge's research into how Nightcrawler's teleportation works accidentally release demonic-looking monsters from some kind of Hell dimension.
  • Broken Base: The series got a fair amount of dislike from those who grew up with X-Men: The Animated Series, but some others liked this incarnation just fine, if not prefer it. Critics attack XME for its lack of fidelity to the source material, its de-aging of all the mutants to teenage and YA versions of themselves, and toning down of violence. Defenders point out that it's the only animated incarnation of the X-Men that isn't bogged down by Wolverine Publicity (the showrunners made it a point of making only one or two Wolverine-centric episodes per season), it also allows proper space and room for an ensemble cast of mutants, where the relationships don't take attention away from the socio-political metaphor and by introducing X-23, it produced a highly successful Canon Foreigner who was ultimately adapted into Logan, the most critically acclaimed and commercially successful of all the entries in the X-Men Film Series, and as such one can argue that Evolution made a more lasting contribution than the original Fox adaptation did.
  • Can't Un-Hear It: Christopher Judge's Magneto voice is viewed as one of the character's better portrayals.
  • Complete Monster:
    • Duncan Matthews started off as a typical Jerk Jock, but becomes something far worse in his final appearance. After Jean Grey dumped him when he described her mutant gifts as a problem, Duncan slowly develops a hatred of mutants. After graduating high school, Duncan got a job at a mining company and harassed mutants in his spare time. After trying to harass a couple of the younger X-Men students, former X-Man Spyke drives him off, destroying his car in the process. In revenge, Duncan steals some mining equipment from his job and he and his friends attack the Morlocks, mutants who live under the sewers. Duncan and his gang throw bombs down the sewer, attempting to kill as many Morlocks as they can and then force the survivors to the surface, so Duncan and his gang can kill them with laser torches. While confronting Spyke, a mutant child named Leech intervenes, trying to protect Spyke, so Duncan decides to try and shoot him.
    • Cain Marko is Charles Xavier's half-brother who uses magic to unlock his dormant mutant gene and became the unstoppable Juggernaut. Resenting his brother since childhood, Juggernaut attempted to kill Xavier, but Xavier defeated him and had him sent to prison. Later, Mystique frees Juggernaut, wanting him to get Xavier's computer Cerebro for her. Juggernaut goes on a rampage, derailing a train, before reaching Xavier's mansion. Juggernaut attempts to kill both Xavier and Mystique after Mystique yells at him for destroying Cerebro. The X-Men and Brotherhood defeat Juggernaut, but Mystique frees him again later. Juggernaut goes on another rampage, heading towards a dam near a small town, attempting to destroy the dam and flood the town in order to wipe out 63,000 lives.
    • Mesmero is a mind-controlling mutant and a servant of Apocalypse. Originally having limited mental powers, Apocalypse boosted his mental powers and promised him more if Mesmero freed Apocalypse. Mesmero takes a job at the circus and encounters the X-Men. Mesmero torments Jean Grey with nightmares to break her will and make her his puppet. Mesmero forces Jean to mind-control other teen X-Men, forcing them to steal 3 rings that serve as a key to the first door imprisoning Apocalypse. Mesmero forces the X-Men he mind-controls to fight their teammates, while he escapes. Mesmero gets the second key by tricking Magneto into destroying a spider creature that was a guardian meant to keep Apocalpyse imprisoned. Later Mesmero allies with Mystique and take her to Apocalpsye's tomb and announces she is the third key. Mesmero tells Mystique to put her hand on the final door, which turns her to stone and frees Apocalypse. Mesmero knows that Apocalypse will kill millions of people to achieve his vision of a better world when freed, but does not care, wanting the power Apocalypse promised him.
  • Die for Our Ship:
    • The Nightcrawler/Shadowcat fans had a bad tendency to do this to Amanda and Lance. Amanda would usually have her canon-characterization inverted where she was suddenly ashamed of Kurt's appearance, when in the show she was often too encouraging and wanted him to be proud of how he looks. Lance meanwhile would be given a massively exaggerated take on his season 1 characterization, to the point he became a full on rapist in some works. In this case, it seems fans would latch onto brief moments where he's shown grabbing Kitty's arm possessively and dialed up until he was a full on abuser.
    • Jean was bashed by Cyclops with Rogue fans pretty much constantly, where she'd be turned into a full-on Alpha Bitch to give the more relatable Rogue a reason to fight for Scott. Scott and Jean also got this a lot from Gambit/Rogue fans, seemingly just to make Gambit and Rogue's relationship seem cooler by comparison.
  • Draco in Leather Pants:
    • The Brotherhood, as a result of how they became completely ineffective as threats and descended into borderline Friendly Enemies with the X-Men during season 2, often get turned into well-meaning misfits who's only crimes are the result of being manipulated by Mystique and Magneto, while ignoring how they were all serious criminals before those two recruited them and even when on their own, could get into serious trouble and cause massive amounts of damage.
    • Lance and Pietro get this the most (though, for Lance this was canon in the second season), with Lance becoming nothing but a sweet and caring boyfriend who's perfect for Kitty, while his temper and antagonism towards the X-Men (which was almost always instigated by himself first) that he demonstrates throughout the rest of the series is downplayed completely. Pietro meanwhile is often turned into a Loveable Rogue at worst in fanworks and romanticized greatly for OC characters to fall in love with. Ironically, Pietro was heroic in the comics, but the show version gave him serious Adaptational Villainy, and while you'd expect this to be a case of people applying the comics canon to the show version, generally it was people who didn't follow the comics who did this.
  • Ensemble Dark Horse:
    • Amara/Magma is the favourite of the New Mutants for being utterly adorable, very likable and extremely helpful in battle when she comes into her own.
    • Amanda Sefton for managing to transcend being a Satellite Love Interest and showing herself to be among the first characters to accept mutants, and being a supportive friend and girlfriend to Kurt.
  • Epileptic Trees:
    • While Ray started out as a Morlock in the comics, the writers never clarified just what his connection with them was in the cartoon, other than the fact they were both mutually familiar with one-another. And the implications of that connection has made his back story even more ambiguous, even compared to the other Recruits, given that most of them never discussed their backgrounds. Most of the fans tend to write him, in fan fiction, as the child of a broken home who ran away and wound up with the Morlocks before being found by Professor X. They also tend to explain that the Morlocks actually pretended not to know him, since he left them they saw it as an act of betrayal and have since shunned him.
    • People on The Other Wiki have made some guesses about Avalanche. Namely, they've guessed he's likely Greek, with 'Alvers' being an Americanized corruption of the name 'Alvez', and that his middle name is 'Domonic' to match his name in the comics.
    • There were a few fans who started guessing when Ristie popped up that - due to the purple hair, English accent and that her name could have just been a more modern version of 'Betsy' - she was going to be revealed as Psylocke.
  • Fanon Discontinuity: "Walk on the Wild Side" gets a considerable amount of hate from fans due to being an incredible ham-fisted "girl power" episode that has multiple characters, most glaringly Scott, acting out of character to shove the message down the audience's throat. Mind you, this show NEVER treated the female characters as less than the males. The tone and characterization are so alien to what the show normally is the episode itself is a borderline Bizarro Episode.
  • Fandom Rivalry: Many fans of the previous cartoon do not take kindly to a comparison between the two, especially ones favoring Evolution.
  • Fanfic Fuel: As a canon High School AU of the X-Men franchise that lasted long enough to introduce a new generation of fans to the franchise, it's natural that a lot of fans grew attached to the setting even as they became more aware of the comics lore, and the characters who never made it. While it maintains the same Sailor Earth friendly nature as the comics (especially given the show-original X-23 and Spyke), it was equally common to see fanfic writers create the "Evolution version" of canon characters, essentially a weird composite of making an Original Character and utilising Adapted Out characters. Favourites for this practice were Emma Frost and Lorna Dane, so much so the latter somehow ended up being listed as a canon character by Fanfiction.net's X-Men Evolution page.
  • Fan-Preferred Couple:
    • Cyclops and Rogue actually became a MAJOR contender from this series, to the point where most of the creators working on it had to be reminded to give Jean more sympathetic character development to make her eventual coupling with Scott more acceptable. Even so, series creator Frank Puar made no secret of the fact that had the show continued into future seasons, Scott and Rogue would eventually become a couple following Jean having a lethal encounter with the Phoenix.
    Puar: We played the relationship card with Scott and Rogue, she makes a play for him, and why not? If anyone has an idea of what she's going through, it would be Scott. He lives in fear of losing control of his powers and killing someone; so does she. He had a lousy childhood; so does she. He always feels isolated because of his powers and of his responsibility; so does she. And he's the one who reached out to her and brought her into an environment of warmth, family and friends. Why wouldn't she make a play for him? She reads Jean's actions toward Scott as mean. Jean is a player, the cheerleader who has everything, and can't make up her mind at what she wants. Scott is an item to her, just like Duncan, and who knows whom else. Rogue thinks Jean is a dumb ass and cannot recognize a good thing when she sees it, so yeah, she's going to make a play on the guy. (Oh, as a minor side note; on the final episode, during the peek into the future, check out who is not included in the group shot and check out whom Rogue lands next to.)
    • Nightcrawler/Shadowcat. It was mostly a side-effect of porting their relationship from the comics to the show. Kurt's canon crush on Kitty prior to dating Amanda and their consistently close friendship after probably helped, along with them being the biggest Ship Launchers in the fandom.
  • Fans Prefer the New Her:
    • A franchise-wide example. Rogue's gothic redesign was quite popular with lifelong X-Men fans and newcomers alike, even more so than her classic flirtatious Southern Belle portrayal. Many viewers felt that it matched her powers far more than her classic personality: she can't touch anyone without absorbing their life-force, so it makes sense that she'd be a bit aloof and standoffish, and wary of expressing physical attraction.
    • Kitty's bubbly Valley Girl persona was widely embraced by fans as an enjoyable new take on the character, and it's now generally accepted alongside her classic portrayal as the plucky "little sister" and resident Audience Surrogate of the X-Men.
  • Germans Love David Hasselhoff: The series is hugely popular in Brazil, having aired during "lunch time" (alongside Static Shock and Justice League Unlimited) in a popular cartoon block on public broadcast TV, with reruns still going even years after being cancelled in North America. Jokes and memes about Evolution (especially regarding the team members' translated names being read out loud by voice actor Sérgio Fortuna during the opening) are still frequent in Brazilian social media.
  • Growing the Beard: The show has decent to average quality in season 1. Near the end of season 2 and the beginning of season 3, however, the show becomes more serious, while still retaining its playful humor, and focuses more on characterization and action. Seasons 1 and 2 focused more on introductions and romance respectively.
  • Ho Yay:
    • Yaoi fans were particularly interested in what Avalanche and Quicksilver did with their free time together living in the Brotherhood Boarding House.
    • Nightcrawler and Cyclops:
      • In "SpykeCam", Evan says, "Scott's pretty stiff, but Kurt usually takes care of that." Can't make this up.
      • The scene where, after the mansion is destroyed and characters have to share rooms, Scott and Kurt emerge from their bedroom with Scott being covered in Kurt's fur.
      • In "Walk on the Wild Side" Scott at one point grabs Kurt and tells him to cancel his plans for the night with a mischievous look, without context it has some heavy homoerotic connotations, something fans were quick to pick up on looking back at it.
    • The entire "Bayville Sirens" montage in "Walk on the Wild Side". Especially the part where Jean and Magma are grinding on each other.
    • Risty asked Rogue to a Sadie Hawkins dance. That is literally what happened; Scott was taken, so Risty suggested that she and Rogue go. This, of course, makes the reveal that Risty was Mystique this whole time VERY awkward.
  • Jerkass Woobie:
    • Evan evolved into this. While he was probably the X-Men's most Jerkass member, he developed into a Woobie during Season Three after anti-mutant sentiment caused former friends to start bullying him. While they were all suffering, Evan was the only one to be shown repeatedly being picked on for his powers, all the while also slowly but steadily losing control of his very visible powers. Eventually, he takes a Mutant harming poison (which were supposed to be a toxin eliminators) and completely loses the hang of his abilities, so the poor kid moves in with the Morlocks as, despite the X-Men's good intentions, the Morlocks are the only ones who can understand his pain. And worse, its unconfirmed if they stop being poisoned by Power8 or if the effects will ever wear off, and they never mentioned if there was a cure.
    • A big reason why the Brotherhood were so popular, and what fuels a lot of their Draco in Leather Pants, Die for Our Ship, Rooting for the Empire fans. They're all criminals even before being recruited, but they're also all basically without any real parental supervision and essentially live in poverty due to none of them having a source of income. To a lot of people, this makes their criminal behaviour and antagonism sympathetic.
  • Launcher of a Thousand Ships:
    • Both Kitty and Kurt are beloved by shippers. It likely stems from their popularity, or their easiness to relate to, but Kitty's pretty much shipped with every guy in the series, and Kurt's shipped with everyone, everyone. You would think save for Rogue, but nope, he's shipped with Rogue, too. Never underestimate fanfic.
    • The Brotherhood also seem to end up with everyone. Well at least Lance, Pietro, and Toad. The Blob aka Fred Dukes, doesn't exist in fanfics.
  • Magnificent Bastard:
    • Apocalypse himself is presented in this series as a far less sadistic villain than usual. Born En Sabah Nur and left to die in the desert because of his status as the first mutant, En Sabah Nur was taken in by the warrior tribe of Baal, trained into their best fighter and destined for greatness. After the slaughter of his surrogate family by jealous, prejudiced humans, En Sabah Nur took the name Apocalypse and swore to bring the entire world under his boot. Using his intelligence to reverse-engineer powerful alien technology to suit his needs, Apocalypse set up hidden bases throughout the world, and even though he was betrayed and imprisoned by his allies at the time, Apocalypse bides his time until he is able to reach out and use the likes of Mesmero to orchestrate his resurrection. Immediately swiping away the X-Men and Brotherhood alike, Apocalypse turns multiple of their number into his "Horsemen" and uses their natural powers to assist him in his plan to transform all mankind into mutants who will live in a utopia of Apocalypse's design.
    • Gambit is a charming thief who joins the Acolytes as one of Magneto's more promising subordinates. Frequently acting as the group's voice of reason and lasting the longest in fights that see his allies otherwise unceremoniously battered, Gambit notably plays a major role in detaining a mystical guardian for Magneto, running the unstoppable beast over with a bus that he then explodes with his power. With Magneto's defeat and the disbandment of the Acolytes, Gambit sets off on his own and kidnaps Rogue to recruit her aid in rescuing his adoptive father from a rival crime family, gradually winning over and manipulating her into volunteering her services to navigate the multitude of traps surrounding his father. A dashing rogue with a heart of gold underneath his duplicitous methods, a vision of the future even shows that he will one day join the X-Men, putting his skills to use on the side of justice.
  • Moe: Amara is so shy and cute that she's incredibly endearing. It doesn't stop her from being a Badass Adorable.
  • Moral Event Horizon:
    • If Mystique didn't cross it when she replaced Xavier and tried to kill the New Recruits, for no reason other than them being unable to fight Magneto, then she did it when she kidnapped Scott, stealing his Power Limiter ruby quartz glasses, and leaving him stranded in the middle of nowhere, repeatedly attacking him and eventually trying to kill him while he's unable to see. All to get back at him for leaving her behind when she refused to tell them where she imprisoned Xavier.
    • Duncan Matthews and his pals went from Jerk Jocks, to earthborn demons by repeatedly physically assaulting Scott unprovoked after he was outted as a mutant, to post-graduation attempted mutant murder with mining machinery and munitions. That last one got them locked up in prison though.
    • There was also the soft-drink manufacturer who unknowingly laced his drink with mutant poison. You can tell he's genuinely surprised... then Mood Whiplash kicks in and he figures he can make a lot of money off the discovery. It ended up not going anywhere, however.
    • Apocalypse was planning on using his machine to turn the populace into mutants... But even he notes that this may kill much of the human population, due to their bodies not being able to take it. He still was willing to go through it.
    • Principal Kelly went from being a possibly bigoted jerk of a principal to a complete bastard when he starts encouraging bullying of mutants and has both the Brotherhood and Duncan team-up to attack Scott so he can convince the school board that mutants are violent and dangerous.
  • More Popular Replacement: Iceman ended up filling Spyke's role as the annoyingly rebellious member of the team. But thanks to the lack of Totally Radical, the character being intentionally an idiot (yet still coming through for the team and being pretty competent) and the fact that he was one of the original X-Men in the first issue means he's better received.
  • Narm: When Professor X is revealed to be Mystique in disguise, the drama of her line "things are about to get much worse" is ruined when there's a pan of everyone else making scared faces that just look goofy.
  • Never Live It Down:
    • Scott was a bit of a stick-in-the-mud but was overall a decent guy. However, "Joyride", where his rivalry with Lance was played up to give Lance an antagonist as he tries to join the X-Men, and as a result Scott became the biggest punching bag for Brotherhood fans. Ironically, he actually made a lot of good points against Lance's membership and did try to be friendly, until Lance's disrespect pushed him into retaliate, but people ignore this and focus solely on how he turned the Danger Room machine on to humiliate Lance in front of others.
    • The New Recruits are only remembered by some fans as Too Dumb to Live assholes, thanks to the same episode. Even though their learn their lesson after, some blame them entirely for Lance quitting since they willingly allowed him to take the blame for their stunts, and as a result some seem to think they were only ever shown as incompetent dumbasses.
  • Nightmare Fuel:
    • Mesmero's introductory episode was this from the beginning to the end in episode 25 (Mindbender). There was no blood, no ultra violence, no huge fights... just him kidnapping and brainwashing a bunch of innocent kids (Jean, Kitty, Evan and Kurt), using them to set off his Evil Plan to wake up his master Apocalypse and slipping unnoticed under their caretakers' watch. And he starts this by entering the kids' dreams and turning them into nightmares. Poor, poor Jean Grey.
    • Blind Alley wasn't much better. Scott gets stranded in a deserted town as Mystique's revenge for him derailing her Evil Plan without his visor, completely unable to even open his eyes or he'll blast everything on sight into nothingness...
    • Apocalypse straddled the line, helped by the fact he wasn't particularly wordy in this continuity.
    • Wanda getting brainwashed instead of character development might have seemed like an easy way out, but when the brainwashing eventually wears off, like comic Wanda's did, there's no telling what kind of hell she will unleash. The girl is a ticking time bomb.
  • Realism-Induced Horror: In the episode Uprising, during a crisis, Mutants are being subjected to bigotry and that people are attempting to kill them just for being mutants, even a mutant child. Mutant powers aside, being the victim of bigotry and hate crimes are something to be legitimately concerned about. The episode shows that people will take extreme measures to deal with what they believe is a problem and how even a child can be a victim of it. Just ask former victims and their family members.
  • Rescued from the Scrappy Heap:
    • Spyke, who after living with the Morlocks, became a powerful, mutant-protecting vigilante that can light his spikes on fire.
    • Jubilee is often regarded as the most useless X-Woman to the general public (comic audiences feel differently though); here however, she's an Ensemble Dark Horse.
    • To a lesser extent as he was only a Base-Breaking Character, but Cyclops lost a lot of fans in the second season thanks to "Joyride" making him the Brotherhood fandom's punching bag. The third season rectifies this as Scott got significant Character Development that put him in line with his comic self more, showing his strong leadership and badassery.
  • Rooting for the Empire: The original Brotherhood members just don't come off as evil to many fans, despite all the horrendous things they did including rigging a train accident to look like heroes one last time and then fleeing when they discover it's going right at another speeding train with eight tankers of fuel. Even with this, however, they spent so much time when in the spotlight being more Chaotic Neutral than outright villainous that many took a shine to them and thought that they'd be far more fun to hang out with.
  • The Scrappy: Spyke was an example of the crew's attempts to bring in a brand new X-Men character for the series who would be the "epitome of cool." This failed so badly (with almost all of the fans being irritated by his "cool lingo"note , overall skater persona, and being kind of a jerk who often forgot the lessons taught to him). Though he got seriously Rescued from the Scrappy Heap over time, generally in the popular census, if anyone brings up his character, it's usually to say what a lame character he was.
  • Seasonal Rot: Season 2, due to its over-focus on romantic side plots, less focus on their battles and less action, though the ending managed to fix that by revealing The Masquerade, leading to it Growing the Beard in Season 3.
  • Slow-Paced Beginning: The first two seasons of the series are mostly episodic, introduces what could be considered too many characters, and drag on for quite a while. But upon the Season 2 finale, and the beginning of Season 3, the series begins putting emphasis on much longer story arcs, and the core themes of discrimination that the franchise is known for.
  • Strangled by the Red String: Liked or not, Kitty/Lance pretty much came out of nowhere. Season 1 had no indication there was any attraction between them, but in season 2 Lance suddenly has a crush on her which she starts to reciprocate shortly after. There was a Deleted Scene where he saved her from some falling rubble which is likely when the writers intended for her to change her opinion of him, but even that was following him trying to destroy the school and the falling rubble was directly his own doing.
  • Strawman Has a Point: Magneto as always. He was presented as an extremist for believing that humanity and mutants couldn't co-exist and his plans to build an army of enhanced mutants to defend mutant kind were presented as villainous...but then when mutants are revealed to the world, they're met with hate, and until the X-Men proved that they could use their powers to protect normal people, the world was readying up to round them up and imprison them. Exactly what Magneto believed would happen. Though Magneto did reveal mutants publicly in the most shocking manner he could, seemingly to encourage this reaction from humans, but this was while they were battling the Sentinel, a machine created by one of the few humans who knew they existed, showing that this view was always bound to exist even without Magneto's interference.
  • They Wasted a Perfectly Good Character: The New Mutants rarely got any focus episodes; Amara, Bobby, Tabitha and kind of Ray (he never gets an episode to himself but plays prominent roles in a couple) are the only ones who do. Jubilee and Wolfsbane got it worst; they were Put on a Bus in Season 3 to keep the cast smaller, not even returning for the fight against Apocalypse. Wolfsbane at least appears in a flash forward in the finale, suggesting they did rejoin the team eventually.
  • They Wasted a Perfectly Good Plot: In the first season, it emerges that Magneto experimented on Kurt when he was a baby, resulting in Kurt's demonic appearance, and he is adamant that Mystique not tell Kurt anything about his past. Head writer and producer Greg Johnson explained that "The way we see it, Magneto experimented on him in an attempt to trigger the X-Gene, and succeeded," but why Magneto is so adamant that Kurt doesn't know the truth about his past is never elaborated on.
  • Toy Ship: Multiple gets shipped a lot, despite being younger than everyone.
  • Unconvincingly Unpopular Character: In the tie-in comics written by Devin Grayson, the kids at Bayville High occasionally refer to Professor Xavier's students as "freaks" or make a big deal about how weird they are...despite the fact that Jean is shown to be very popular at Bayville in the actual TV series, and Scott and Kurt (while not particularly popular) are shown to be generally well-liked, and receive their fair share of romantic attention from girls. While it's once mentioned that Jean is considered "okay", and someone makes reference to having a crush on Scott, it comes off as a bit odd that anybody would consider the group "freaks" as a whole—particularly since the comics are set at a point before anyone has any idea that they're mutants.
  • Ugly Cute:
    • Nightcrawler's blue form is still quite appealing, even with the fur and pointed teeth. It turns out Amanda Sefton feels the same way, as she ends up preferring his natural form.
    • Toad is given a gawky appearance and is said to not bathe very often, but his design is actually rather cute.
  • Unintentional Period Piece: The fashion, technology (particularly a camera Spyke uses in a season 1 episode), noticeable emphasis on sports, and some lingo make it apparent that the series takes place in the early 2000s.
  • Unintentionally Unsympathetic:
    • Lance's romantic subplot with Kitty starts with him saving her life — from an accident that he caused. He had also previously attempted to attack Kitty, and due to the nature of his powers, he tends to cause a lot of collateral damage (sometimes near schools populated by children who are never confirmed to have gotten out alive). To some people, all this makes it kind of hard to believe that Kitty would want him for a boyfriend. This also puts him in the somewhat unusual situation of being a common victim of both Ron the Death Eater AND Draco in Leather Pants.
    • Jean in the infamous "Walk on the Wild Side". Her complaints about often being mistreated because of her gender or being considered a Damsel in Distress are a complete Compressed Vice - considering she was put in charge many times before and shown respect by most of the others. It makes it come across as Wangst, especially since her tantrum is kicked off when Scott saves her from a falling boulder.
    • Kurt in Season 4 for trying to persuade Rogue to be okay with him keeping the petrified Mystique in the manor. Here's the deal; Mystique treated Rogue far worse than Kurt. Kurt was only accidentally abandoned as a baby when she was fleeing from the wolves - after she had expressed fury at what Magneto had done to him. And besides masquerading as his principal and later Professor X, he didn't really suffer because of her. Rogue meanwhile? Mystique knowingly abandoned her with Destiny and, when her powers awakened, resorted to Gaslighting her to convert her to the Brotherhood. Then she posed as a friend to become Rogue's confidant for months, ostensibly to spy on the others and break into the mansion. Finally, when Rogue was still reeling from the trauma of that revelation, she willingly worked with Mesmero to Mind Rape Rogue into draining her friends and then reviving Apocalypse. This also gives Rogue massive second hand guilt over the world being endangered, and Kurt knows all of this - yet he brings the petrified statue back to the manor even when the reason it was sent away was because Rogue was understandably bothered by having a tribute to the woman who used and abused her multiple times. While the attempt was at Both Sides Have a Point (Kurt seeing more of Mystique's potential for good than Rogue), Kurt comes across as insanely insensitive to Rogue's trauma. Thankfully as of the finale, he tells Mystique to get lost along with his sister.
  • The Woobie:
    • X-23 is a clone of Wolverine that was raised from childhood to be a living weapon. She has never had any friends and lived a torturous life without any opportunities to feel happiness. In her first appearance, she breaks down in Logan's arms.
    • David/Legion, who was first told by his mother that his father Xavier abandoned him, then he moved to a new place where he had no friends, and then was slowly taken over by an alternate personality. An alternate personality that kidnapped and held him hostage in a castle. Then he gets permanently taken over when his dad tries to save him. Poor kid. Because the series was cancelled after Season 4, this becomes a case of The Bad Guy Wins, at least as it stands - there are hints he could've been still saved had the show continued...
    • Rogue cannot touch anyone without causing them extreme pain or possibly even killing them, both of her mothers seek to use her to their own ends, and one of the boys she's in love with is dating someone else, and the other was put in a coma because of her powers.

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