Angel is featured heavily in all the promotional material, as part of the whole "the original X-Men team in the comics finally together in film". He only has two or three scenes: he refuses the cure and runs (flies?) away; he very briefly shows up at the X-Mansion for the sole purpose of allowing them to state categorically that the school is still open; and finally he saves his father's life during the final battle. He does nothing in between.
The same can be said of Colossus — he has one line (which is about as long as both of his two lines in X2 combined) and he's really only in the film for the Fastball Special.
It should come as a surprise to nobody who saw the movie that several scenes were deleted from the final cut—not unusual in this movie series, but much more noticeable here. This obviously affected how much screen time several characters got.
Cyclops also counts, his screentime is greatly reduced due to James Marsden's other commitments.
All There in the Script: Happens to a bunch of characters. For instance, the Asian mutant with the purple hair is indeed identified as Psylocke in the commentary, but is never called that (or her civilian name, "Betsy") onscreen.
A Minor Kidroduction: The film starts with a younger Professor X and Magneto visiting Jean Grey as a child.
Antagonist in Mourning: Magneto sincerely grieves over Xavier's death and cuts off his Dragon Pyro's irreverent talk about the deceased abruptly. As in most versions of X-Men, Xavier and Magneto were very close friends who eventually found themselves on separate sides due to their ideological differences.
Ballistic Bone: Spike pursued Wolverine through the forest at one point. Some bone spikes were thrown during pursuit, and after that two others were used in melee combat, leaving a pair of holes in Wolverine's shirt.
Barcode Tattoo: Magneto's katzetnik, used to show off his history of being mistreated.
Beam-O-War: The film has Iceman and Pyro using beams of ice and fire, respectively. When Pyro starts to gain ground, Iceman abandons the beam strategy and coats himself in ice armor, allow him to just walk over and take down Pyro with an old-fashioned headbutt.
When a cure for mutants is introduced, Magneto is primarily wary that humans will 'draw first blood' and use it to forcibly strip mutants of their powers—which is exactly what they do. Unfortunately, he, the Brotherhood and Jean Grey then go on to launch an attack on the cure-production facility (tearing the Golden Gate Bridge off its foundations in the process) with the stated intent of destroying the cure's source — which happens to be an innocent teenage boy who is himself a mutant, thus giving the humans every reason to believe the mutants are exactly as dangerous and destructive as feared.
Also when the heroes are discussing taking the cure.
Storm "I don't believe this. What sort of coward would take that just to fit in?" Beast "Is it cowardice to want to be free from persecution? Not everyone can blend in so easily; you don't shed on the furniture."
Broken Angel: A young Angel tried to cut his wings off to avoid being rejected by his father.
Brought Down to Normal: The plot of revolves around a serum created from a mutant that imposes this trope on any other mutant around him. Throughout the movie, several characters take the serum, either forcefully or willingly. Major characters include: Mystique, Rogue, and Magneto. In Magneto's case, it's revealed in The Stinger of The Wolverine that it may not be permanent.
There is an alternate scene where Rogue doesn't take the serum.
Cape Busters: The military is eventually equipped with "cure weapons", firearms and indirect fire weapons that contain a serum which disables mutant powers on contact. Or does it? They even manufacture plastic and glass versions of the weapons to fight Magneto. As appropriate for the themes of the movie, the serum permanently disables mutant powers and its use as a weapon is highly controversial.
Callisto merges the powers of the comic characters Caliban and Quicksilver. Her leadership role and personality (which isn't all that fleshed out in the movie, but overall it's pretty consistent with the comics) are the only traces of the comics' Callisto.
Jean Grey and Phoenix were separate characters in the comics, but were rewritten into separate personalities in a single body for the movie. But whether Phoenix was a separate entity or just Jean's Superpowered Evil Side depends on who's writing.
Covers Always Lie: Several of the posters showed Angel clad in an X-Men uniform and acting as part of the team. Not only does Angel not wear a costume in the movie, he doesn't even officially join the X-Men either.
Cyclops, though there's a reason. Rogue, as well, she had fairly large parts in the first and second movies, but her storyline in this movie remotes to her being jealous of Bobby and Kitty and taking an apparent cure. Part of it was also because Halle Berry didn't like Storm's comparatively smaller role and demanded a larger part. But objectively speaking they both were shafted.
Dr. Kavita Rao. Gets about thirty seconds of screen time, three lines in total, and then is Killed Off for Real. Most of her role from the comics (like holding the press conference) is taken over by Angel's dad. She was never a major character to begin with, and was a very recent creation when the movie was made, but still.
Psylocke, she usually has a fair amount of input on the plot in the comics.
Doing in the Wizard : The Juggernaut is simply a mutant who was born with his abilities. In the comics, he gets his powers and armor from a mystical gem. The Phoenix is just Jean Grey's alternate personality, rather than a god-like cosmic entity. Though to be fair, the Phoenix originally was just Jean in the comics before it was Retconned into being a creature from space.
Mystique is Magneto's primary dragon for part of the movie.
It's somewhat unclear who takes over as Magneto's dragon after Mystique's departure in the third film as there isn't a clear-cut second in command. The two top candidates would be Pyro, who is the only remaining member of the Brotherhood who was with Magneto prior to the beginning of the movie, and Callisto, who was the apparent leader of the Morlocks before they became Magneto's new Mook army. A case might also be made for Juggernaut, though he fits better in the role of The Brute.
Notoriously, the film eliminated several franchise regulars, with arguably the most controversial example being that of Scott Summers, aka Cyclops. Despite acting as the team's field leader and, within the regular comic series, their linchpin since inception, he's quickly killed off-screen within the first 30 minutes of the film by his newly resurrected fiancee, Jean Grey. As though that wasn't bad enough, his death barely registers with the rest of the cast later on in the film, with only a brief mention by Professor X who doesn't seem overly perturbed by the loss of his surrogate son.
To some of the general public, Cyclops' anti-climactic death might not have been that big of an issue as his screentime got shafted in the previous 2 films in favor of Wolverine, who acted as the series' cinematic alpha hero. However, for fans of the comics, the death was also a slap in the face of sorts since the film's plot was heavily influenced by the comics' extremely well-regarded "Dark Phoenix" storyline that focuses on Jean and Scott. Within the context of the film, that story became a secondary plot thread, and Wolverine was substituted in as the romantic/heroic lead in light of Scott's less than stellar death.
Also, Professor X is killed off midway through the film. Coupled with the fact that Rogue and Mystique were both Put on a Bus and Jean had basically removed herself from the X-Men/Brotherhood fray, you have a climax that barely features any of the characters from the previous two movies.
Also of note are Kid Omega, Arclight, Psylocke, and (presumably) Juggernaut, all of whom unceremoniously fall victim to Jean Grey's psychotic "burn everything" episode near the film's conclusion.
Dungeon Bypass: Both Kitty Pryde and Juggernaut take the direct route to Leech's chamber. Kitty runs through the walls by phasing, while Juggernaut runs through them by running through them.
Dying as Yourself: The film has Jean changing from some nasty veined greeny-grey skinned demon with black eyes to herself, lit from behind somehow and smiling peacefully when Logan kills her.
Just before the credits roll a depowered Magneto is seen sitting in the park, in front of a table with (presumably) metal chess pieces. He holds his hand forward, and one piece tilts ever so slightly before the screen goes black.
Also, it's made fairly clear that Professor X has possessed the body of the brain-dead man they showed earlier on in the movie, who is apparently his twin brother.
Equal-Opportunity Evil: The members of the Brotherhood of Mutants are very diverse. Psylocke and Quill are Asian, Arclight is Hispanic, Spike is black, and that's not even counting all the nameless Mooks.
Even Evil Has Standards: Magneto reacts with horror when he notices that Phoenix is about to kill Charles Xavier. In addition, when Pyro indicates that he would have killed Xavier if Magneto commanded him to do so, Magneto immediately rebukes him for the comment, telling him Xavier had done so much for mutants and that his greatest regret was Xavier's death.
Eye Awaken: Not involving a death, but something similar happens at the end. Magneto, who has lost his power, reaches a hand out toward a metal chess piece, which twitches ever so slightly just before the credits roll.
Fastball Special: Because it wouldn't be right or proper not to include the move in the series, — during a fight against a simulated Sentinel — has Wolverine turn to Colossus and ask “How’s your throwin’ arm?” Audiences cheered. The move itself, however, it was considerably altered, resembling more of a hammer toss than a fastball throw, to compensate for the fact that Hugh Jackman is like fifteen feet tall compared to comics Wolvie. The second time... Magneto gets involved.
Final Battle: Magneto's attack on the Alcatraz research facility.
Finger Twitching Revival: Played with at the end. Magneto's fingers cause a chess piece to twitch, implying his powers are returning.
Foiler Footage: For the ending, they filmed the "Bobby discovers Rogue" scene both ways. That is, one where she took the "mutant cure" and one where she didn't. The commentary said that a poll was taken on set about whether she should take the cure or not.
The Foreign Subtitle: In Japan the films subtitle was changed from The Last Stand to Final Decision.
Freakiness Shame: When Mystique is de-mutant-ed against her will and left looking like a naked Rebecca Romijn, Magneto sighs regretfully as he leaves her behind, "She used to be so beautiful…"
Futile Hand Reach: Magneto does this towards Jean after he's been zapped by the anti-mutant drug.
Genre Savvy: When the army learns Magneto is on the warpath again, a sequence shows them trading in their metal equipment and weapons for plastic variants, so he can't exert his influence on them. A scene in the final battle has him discovering this and muttering "Plastic...they've learned."
Grand Theft Me: At the very end of the credits, there is an Easter Egg scene in which Professor Xavier, who was killed during the movie, is revealed to have implanted his mind into the body of a man who had been earlier revealed to have a functioning body, but no working mind. It is ironic because Xavier had lectured to a class earlier in the movie about the ethical dilemmas involved in such a transfusion of soul, so to speak.
Groin Attack: When fighting a mook who just keeps regenerating the limbs he's cutting off, Wolverine kicks him in the balls and quips "Grow those back."
Hide Your Otherness: The film starts with a little Angel who tries to cut off his own wings in his desperation to be normal. Considering that he *did* cut them off then, but still have them later in the movie, they must have kept growing back.
Hold the Line: Wolverine says this trope almost word for word as he commands the X-Men to stand their ground and protect Leech, the source of the cure at Alcatraz.
Humanity Ensues: The film has this happening to mutants who are exposed to the "cure".
I Just Want to Be Normal: A large part of the plot revolves around a cure for mutants. As a result, some of the characters must contend with whether or not they actually want to be normal and take the cure. Eventually, Rogue decides it's what she wants and takes the cure; however, one alternate ending shows her not taking it, and holding hands with Bobby wearing gloves.
Indy Ploy: To take down Juggernaut, Shadowcat goads him into charging at her and Leech. Leech's power nullifies the Juggernaut's, and when he slams into the wall he gets knocked out.
Inertia Is a Cruel Mistress: Kitty uses this against Juggernaut. She realizes that the kid she's been sent to rescue has the ability to suppress powers. Since Juggernaut's power makes him unstoppable, taking that power away without his knowledge means that he expects to just crash through the next wall.
Leech. The movie ditches his defining trait of not passing for normal and not being able to do anything about it because most mutant powers don't work on him. Also, his powers no longer temporarily nullify whoever he touches, he has an area of effect that fully humanizes whoever enters it. Granted, it serves as a better justification for using him as a source for The Cure, as using the original comic book plot would have left no screen time for the Phoenix plotline.
Internalized Categorism: The movie starts with a little Angel who tries to cut off his own wings (and maybe he did that quite often) in his desperation to be normal. Later, his father tries to help him get "cured" of having white wings to fly with. Angel changes his mind at the last minute, however, and later uses his flight to save his father's life.
It's worth noting that in that scene, Jean had been in a majorly unstable state thanks to the Phoenix but hadn't actually fought during the Alcatraz battle... until the military's attack, which made her snap.
I Warned You: Professor Xavier says this to Logan after Phoenix escapes, having been awoken by Logan before Xavier could bring Jean Grey back to normal.
Japanese Tourist: When Magneto detaches the Golden Gate Bridge and moves one end onto Alcatraz Island, there's a cut to a group of Japanese tourists who flee, leaving one astounded man behind a camera on a tripod.
Jumping Off the Slippery Slope: Discussed between the president and Beast, when they debate weaponizing the cure as a safeguard against dangerous mutants. The president tries to rationalize it as a extreme circumstance, to which Beast responds by pointing out how quickly such a justification can snowball before resigning. The president ends up doing just that when Magneto's mutant army shows up, but by the end he's climbed back up and rehired Beast to help smooth things out again.
Jump Scare: By way of the the score. Right before the credits, Magneto starts to move a metal chess piece. Just when you think it'll go more into the scene, BOOM! Smash cut into the credits using the score.
Karma Houdini: Magneto is last seen, supposedly broken, sitting in a San Fransisco park playing chess. Presumably during the confusion at the end of the battle of Alcatraz he managed to slip away, instead of going back to prison to pay for all the death and mayhem he caused. The end of the movie implies his depowering won't even be permanent, making this even more of an example.
Karmic Transformation: In X-Men, Magneto tried to find a way to turn normal humans into mutants. He used this technique on a Senator who hates mutants but the guy soon died from complications. In this film, this is turned around on him, with the humans developing a "cure" and Magneto being robbed of his mutant powers. Though the final scene reveals that the cure is already starting to fail, as he's able to make a metal chess piece move slightly.
Kick the Dog: While Magneto may have been a complex Anti-Villain with sympathetic goals, his slide toward the Moral Event Horizon is punctuated with increasingly cruel kick-the-dog moments. In particular is when Mystique is hit with a "cure dart" and turns suddenly into a beautiful, stricken, and supremely vulnerable human woman. And then he promptly abandons her without a second thought. Not to mention the fact that she had just saved him.
He also gets major dog-kicking points in the scene where his forces fight against the government. He uses Chess Motifs, telling his protege, Pyro for them to wait until the pawns (his other followers) exhaust themselves. In this moment, like the above scene, Magneto violates his own standards of decency, since if nothing else, he supposedly cares about mutants.
When Beast approaches Leech, his powers are drained. Apparently his powers include "being hairy", because his hair withdrew into his body as he got close, and immediately grew back when he stepped away.
Same happens to Mystique when she gets her shot of Applied Phlebotinum, she loses her shapeshifting ability and looks like a normal human again. A bare naked normal humanRebecca Romijn at that. note The second example explains the first based on the events of X-Men: First Class, where it's shown that Hank's hairy appearance is originally the backfired result of an attempt to use Mystique's genes to make himself appear totally human (his mutation had only previously affected his appearance in regards to his weirdly large feet).
Magic Pants: Jean Grey (as Dark Phoenix) is disintegrating everyone and everything around her, and Wolverine gets near her. Her power disintegrates his shirt (and hischest), but not his pants. (that one was enforced by the ratings board: Hugh Jackman shot the scene wearing flesh-colored pants, but the censors requested digital pants to be added back onto Wolverine in order to keep the PG-13).
Psylocke appears for a bit, though mostly in the background, before turning into Ludicrous Gibs.
Kid Omega lasts quite a bit, kills one character and almost does so with a second.
Multiple-Man's only active part in the plot is distracting the military while the Brotherhood goes to San Francisco.
Monumental Battle: The climax takes place at Alcatraz and the demolishment of the Golden Gate Bridge.
Monumental Damage: Magneto rips the Golden Gate Bridge out of its usual position so the Brotherhood can cross it to reach Alcatraz Island.
Monumental Theft: Magneto takes the Golden Gate Bridge and relocates it to Alcatraz.
Mooks: The film is based around Magneto raising an entire army of mutant mooks. He even lampshades using them as, in the final battle, when he sends his first wave of defenders (who make the classic mook mistake of charging impulsively at the attackers), he calls the defenders "pawns".
My God, What Have I Done?: The film features Magneto saying the line, when he finds himself on the other side of the Mutants Vs. Humans war he's been pushing for and Phoenix finally goes crazy and starts killing people.
Mythology Gag: the last fight of Phoenix takes place in the bay of San Francisco, precisely the place where the reborn Jean Grey re-emerged as the Phoenix in the comics.
Neck Snap: Mystique neck-snaps a guard with her feet since her hands are chained to the ceiling.
Never Say "Die": An unusual in-universe example. When Wolverine is questioning Jean about what happened to Cyclops, she refuses to actually say he died. How much of this is guilt or foreshadowing is up to interpretation.
Not His Sled: In the comic book version of The Dark Phoenix Saga, Wolverine managed to open his way to Jean, and she accepted her fate and requested him to kill her. But he goes back at the last moment: he loves her, he can't bring himself to kill her. Same thing on the animated series. Same context in the film... completely opposite outcome.
Phlebotinum Bomb: Arclight's shockwave. She was able to target only the soldiers' guns. (In the comic books, she doesn't appear to be able to fine-tune it like that... and wouldn't have bothered sparing the soldiers, anyway.)
Powered by a Forsaken Child: The mutant cure is distilled from Leech's blood, though they hope to eventually artificially synthesize it. Unlike other examples, Leech is treated rather well and seems fine with the arrangement.
Power Levels: Mutants were inexplicably given power levels that everyone was aware of from 1-5 with Professor X and Magneto as 4s and Jean Grey being the only known 5. Apparently, Calisto can specifically "sense" these power levels- again having no prior mention in the movies or anywhere else in the X-Men universe.
Power Nullifier: Leech could to not only nullify mutant powers but also give even the most deformed mutant a normal human appearance. His DNA was used to create the mutant "cure" which Rogue takes in order to be with Iceman. Magneto's scene seems to imply that the cure might not have been permanent, at least in people who really didn't want to be cured.
Powers Do The Fighting: The film has a scene where Jean Grey/The Phoenix strolls across the battlefield, and anyone that gets near her is instantly obliterated. As in separated molecule by molecule.
As the DVD's deleted scenes reveal, the film was originally poised to have one of these: "Mr. President, shut the fuck up!" The final cut of the film is actually the least profane of the trilogy, with not even a "shit" making it through. The most TV-unfriendly word in the movie is "dickhead".
Prison Ship: The government imprisons Mystique in a special mobile prison built on a semi-trailer that is constantly moving; thereby making it harder for the Brotherhood to locate her and stage a rescue.
Proscenium Reveal: The film opens with an action-packed scene in burning city ruins, but it is revealed to be just a Danger Room simulation after the Fastball Special.
In a deleted scene, Wolverine fights Juggernaut for the first time and actually drives his claws through Juggernaut's arm. Juggie doesn't even flinch, triggering an immediate Oh Crap moment from Logan—that he lampshades after Juggernaut curb-stomps him.
Later in the film, Logan fights a mutant who can regenerate lost body parts. After a couple of unsuccessful attempts with his claws, Logan decides to Take a Third Option and goes for a more traditional weak spot.
Bolivar Trask is played by an African American actor, while his original comic book incarnation was a white guy.
Kid Omega also becomes Asian American, though this is definitely a case of In Name Only since he has almost nothing in common with his comic counterpart. He had much more in common with Quill, and is even referred to as such the director's commentary. This would still make this a race lift, since Quill was white too.
Callisto is also played by a dark-skinned Latina actress.
Red Shirt Army: The army of mutants, less than a dozen demonstrated any special ability except rushing forward blindly, to the point that the previously completely ineffective human army kicks their butts. It was mentioned that those mutants were the ones with lame powers. Plus, the army had power-neutralizing weapons. A flesh wound in the shoulder turns Joe Random Rock Thrower into Joe Blow. And for the most part the mutants were all untrained civilians. The most they could do was rush forward blindly and get cut down.
Related In The Adaptation: Inverted. There is no relationship between Xavier and Juggernaut while they are step brothers in the comics (with Juggernaut's hatred of Xavier being his major motivation).
Running Gag: Likely unintentional, but whenever Wolverine tries to confront Magneto, he ends up thrown through the air.
Self Destructive Charge: Wolverine's relentless advance towards Jean probably counts - his Healing Factor kept him regenerating in the face of the telekinetic assault, but still... Some suspect it was only his Magic Pants that kept his legs from getting the same treatment.
Sequel Hook: Despite being the final chapter in a trilogy, the film has a potential sequel hook in its final seconds; the de-powered Magneto, homeless and alone, sits at a (steel) chessboard in Central Park vainly trying to make the pieces move; one pawn wobbles, almost imperceptibly, in the instant before the shot cuts to Brett Ratner's director credit. There is even a second hook after the credits, showing that Xavier survived in the Chekhov's Gun. (eww.)
Sequel Non-Entity: Nightcrawler's absence was handwaved in the X2 video game, so the die-hard X-Geeks knew. All us normal people were left in the dark. (in real life, Alan Cumming didn't want to use that painful make-up again without Bryan Singer at the helm).
Shapeshifter Guilt Trip: Mystique tries this on her captors. She transforms into the President and threatens to have them all court martialed if they do not release her, and then a little girl who begs and cries to be let out. She finally turns mockingly back into herself when one of the guards threatens to empty a can of pepper spray in her face if she doesn't knock it off.
Shoot the Dog: When Jean Grey has completely lost control of her alternate personality "The Phoenix", Wolverine is the only one with the fortitude (both moral and physical) to put her down in the end, despite being in love with her. To take the edge off the trope, she regains enough control to request that he kill her. In the original comic saga, Wolverine pointedly can't bring himself to do it.
Skyward Scream: Wolverine does this after reluctantly killing Jean Grey/Phoenix.
Small Name, Big Ego: Kid Omega/Quill, who genuinely think he's threatening to Magneto at the gathering of mutants when he extends his quills. His sole kill in the movie is killing a single, crying woman by giving her a hug then extending his quills. Then he gets killed in an action that could be charitably called an afterthought.
Status Quo Is God: The film seemed like this. During the movie, several characters died (including Professor X!) and many more were "cured" of their powers. Two scenes at the end hint that 1. Xavier downloaded his mind into a catatonic body and 2. Magneto and the others are recovering their powers, meaning the only changes that stick are Scott and Phoenix's deaths. And since Phoenix came back once...
The Stinger: Professor X transfers his mind into the man with the coma...
Strong as They Need to Be: Wolverine pulls this off when he faces down Dark Phoenix in the climactic scene of the movie. His healing powers are inexplicably multiplied to the point where he can walk up to Phoenix (who by this point had already atomized several main characters and the entirety of Alcatraz island), taking multiple psychic blasts which flay the muscles from his bones only to fully regenerate in less than a second. Keep in mind that this version of Wolverine took some time to heal from a single gunshot or being hit by a log. This was so egregious that it got a Word of GodRetcon, stating that Phoenix's out-of-control abilities also amplified the powers of nearby mutants. It's also been surmised that Jean was Fighting from the Inside, not letting her full power (which could easily turn Wolverine, adamantium skeleton and all, to vapor) be brought to bear.
Stupid Sacrifice: Magneto sacrifices his troops against soldiers he knew were armed with the serum, rather than have Phoenix just nuke the island from afar or crush the entire island and everyone on it with the Golden bridge, or form the metal of the bridge and cars into a swarm of shrapnel and eviscerate all the guards. Phoenix's inaction was at least explained in a deleted scene where she simply refused to help. The rest not so much.
Superpower Meltdown: The film features this in the form of Phoenix. Sure, she had total control of her powers, but she was still going completely batshit. At least until she asked Wolverine to kill her and end it.
Taking the Bullet: Mystique throws herself in front of a dart containing the mutant "cure" that's fired at her lover Magneto. Despite this selfless act, Magneto abandons her because the dart has turned Mystique into an ordinary human.
Tattooed Crook: Like most Omegas, Kid Omega and Callisto have many tattoos.
The Force Is Strong with This One: The film had Callisto who could detect other mutants and ascertain their relative "power-levels" on a 1-5 scale. Only one level 5 has ever existed, and when she tells Magneto that she just became aware of a "level 5", he immediately knows that she refers to Jean Grey's "Phoenix" personality.
Too Fast to Stop: Kitty Pryde is getting Juggernaut to chase her through the walls of the Alcatraz laboratory, right up to the room where Leech is. Since she can't phase anymore, she moves close to the far wall and when Juggernaut comes bursting through the last wall, he runs full steam towards them. Unfortunately for him, Leech's power kicks in and he slams into, not through, the wall with enough force to knock himself out.
Tuck and Cover: Colossus shields Rogue this way in the Danger Room simulation, however this is also so that she can get his steel skin for further protection.
Twenty Minutes into the Future: "The not too distant future" subtitle gets a bit confusing by the time this movie happens. Simply because two scenes occur before the opening credits, and they are stated to be "10 years ago" and "20 years ago." It is never specified when exactly those two scenes were supposed to be 10 and 20 years ago from, now or from the not too distant future. (Confused yet?)
Verb This!: A variation occurs towards the end, Wolverine is fighting one-on-one against a mutant with regenerating limbs. After the third or fourth attempt at dismemberment, he changes tack and kicks his adversary in the crotch instead, remarking:
Villain Team-Up: The film had Magneto convince Jean Grey in Phoenix form to work together; sadly, this was because Jean didn't trust Charles Xavier and killed him while Magneto watched.
Vulnerable Convoy: Magneto attacks the prison convoy transporting Mystique, Multiple Man, and the Juggernaut.
We Have Reserves: Magneto takes a step away from his usual place as an Anti-Villain to order a group of weak mutants to lead a charge. He holds back his eager new apprentice Pyro from joining the charge, telling him "In chess, the pawns go first." When they get mowed down (revealing the other side's secret weapon, guns that shoot Power Nullifiers), he comments "That's why the pawns go first".
Taken to new heights with Kid Omega, whose abilities are... retractable inch-long spines. Apparently inspired by comic character Quill. But while Quill can usually shoot these spines, these just... stay there. While this could be a devastating power if you were intent on killing everyone at a chronic cuddler retreat, in combat with people with guns, psionic powers, and various other super-abilities, it's kinda weak. Despite this, he acts as though he is an impressive mutant, using his quills for intimidation purposes on multiple occasions. (Not a bad idea, but useless in the circles he travels in.) It's made worse by the fact that his only on-screen kill is a defenseless, crying woman whom he comforts with a hug then impales on his spines. Some sources describe the spines as poisonous, but still not all that interesting note The comic version of Kid Omega is decidedly more interesting but just as useless: he has a "transparent mind" that makes all of his thoughts visible to passersby. When amped up by performance-enhancing drugs, however, he reveals himself to be an incredibly powerful psychic. Of course, he kept that amped-up level, making his day-one weak powers more a part of his origin story, like pre-Super SerumSteve Rogers' frailty. There's a reason he's called Kid Omega - Omega is the highest class of mutant powers. Scarlet Witch and Franklin Richards are Omegas. Apocalypse isn't. Every time Kid Omega gets bored with ascending to a higher plane of existence, he reforms his body from its current state as goop in Beast's lab and wreaks global scale havoc. If he had real ambition instead of being a brat throwing (incredibly dangerous) tantrums, he'd stand uncontested at the top of the X-Men's rogue's gallery. The mystery of why the movie makers would even apply the name to a porcupine dude is something still occasionally discussed..
And Phat, whose power is...He gets fat. Then thin again.
Iceman and Rogue. Iceman seems disappointed that Rogue "cured" herself, even though she did it for both of them. It's unknown what their relationship is now, especially since the cure is temporary.
Iceman and Kitty is hinted at, especially during the ice skating scene.
With Great Power Comes Great Insanity: Jean Grey in her manifestation as Dark Phoenix. Although it is explained that she was already mentally unstable as a girl and her massive powers had to be reduced for her own good and that of everyone around her by putting mental blocks into her psyche. When these were removed, she started killing people with her mind. (This is actually closer to the original Phoenix story than the later comic and adaptation stories that portray Jean as having been Touched by Vorlons.)
Speaker: This cure is voluntary. Nobody's talking about extermination.
Magneto: No one ever talks about it; they just do it. And you go on with your lives, ignoring the signs all around you. And then one day, when the air is still and the night is fallen, they come for you.
Speaker:[interrupts] Excuse me-
Magneto: Only then do you realize that while you're talking about organizing and committees, the extermination has already begun.
Magneto is exploiting this trope, however: he is using fear of genocide to widen the divide between mutants and humans and perpetuate his war against humanity, ostensibly to protect the mutants from just such an extermination.
Would Hurt a Child: Magneto's assault on Alcatraz involved killing Leech. When Juggernaut is ordered to do it, he replies "With pleasure."
It makes a bit more sense when you consider the original ending of the movie. When Magneto is at the park bench at the end, Mystique was supposed to be sitting next to him, implying that Magneto's rejection of her and her subsequent betrayal were both actually staged to lower the defenses of Alcatraz Island later.