The third movie in the X-Men series involves someone finding a "cure" for mutant genes, causing Magneto to start recruiting for a mutant uprising. Also, Jean Grey gets better (guys, It Was His Sled!), but evidently Came Back Wrong, because now she can kill you with her brain. Rogue takes the cure voluntarily, on grounds that she Can't Have Sex, Ever. The X-Men move to defend the cure-making facility from Magneto's forces, and eventually "cure" him, which puts an end to his crusade. Unfortunately, Jean stays Ax Crazy, so Wolverine has to kill her, after which he returns to the Xavier Mansion to help Storm lead the next generation of X-Men.
Advertised Extra / Billing Displacement: Angel is featured heavily in all the promotional material. 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 actually shorter than his one line in X-Men 2) 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.
All There in the Manual: To explain things that weren't explained in the movie itself (such as why Nightcrawler was absent), a video-game was made that took place between X2 and X-Men: The Last Stand that filled in the gaps.
Armor-Piercing Question: Not technically a question, but "You need to tell me what happened to Scott" certainly counts.
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."
Call Back: When Mystique is screwing with the guard on the prison truck, she briefly turns into Jason Stryker's "little girl" avatar from the second movie.
Casting Gag: Former soccer player Vinnie Jones as Juggernaut, whose American football design is deliberately played up with his "unstoppable" mutant power.
Vinnie Jones is a violent musclebound psychopath. Ergo, Juggernaut.
Couldn't Find a Lighter: In the Danger Room Cold Open, Wolverine uses holographic burning rubble left by an attacking Sentinel to light his cigar. Yes, Wolverine is so Bad Ass he can light a cigar off flames that don't actually exist.
Deadly Dodging: Kitty seems to be a master at this. Even without her powers.
Deadly Hug: How Wolverine finishes off Phoenix. Also how Kid Omega/Quill kills that lady doctor.
Demoted to Extra: 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.
Also, Cyclops (then again, James Marsden was busy with something else).
Dropped a Bridge on Him: Quite a lot: Cyclops, Xavier, Jean, plus Rogue and Magneto to the lesser degree (depowered rather than killed). Fans were particularly put off by Cyclops' death, coming as it does ten minutes into the film and his character already having gotten short shrift in the franchise.)
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."
Headdesk: The Juggernaut has Shadowcat and Leech cornered and charges them. Unfortunately, Leech's power nullifies his, so the two duck under his rampage and Juggernaut smashes the wall, knocking him out cold. Possibly justified due to Juggernaut's predictability, and he probably wasn't aware that his powers would get shut off so abruptly by Leech.
Hoist by His Own Petard: Pyro mocks the protective headgear worn by Magneto and Juggernaut. How is he taken out? Iceman headbutts him.
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 sorce of the cure at Alcatraz.
In Name Only: Quite a few, kicking off the tradition of "use character A with powers of character B, when simply using character B might've been a better idea" that the next movie sadly inherits.
Callisto. She's not scarred or one-eyed, she has a mix of Caliban's and Quicksilver's powers and not her own hypersensitivity (which would have had pretty much the same Plot Device effect).
Psylocke. She's somehow a Mook now, already non-British (while the movie continuity avoids and RetCons all things magical and alien, meaning that there is no Siege Perilous in this world) and all that. At least her hair is purple... small consolation. The only power she uses in the movie is the shadow teleportation granted to her by the Red Dawn, but not her own (weak) telepathy or (highly advanced) telekinesis.
Kid Omega is Quill.
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.
Phoenix. She uses her heightened powers approximately two times through the entire movie and almost doesn't speak at all, leaving out all of the Character Development so integral to any version of the Phoenix Force in the comics, mostly just standing behind Magneto, looking ominous.
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.
Karma Houdini: Magneto is last seen, supposedly broken, sitting in Central 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.
Karmic Transformation: X-Men: Magneto tries turning humans into mutants. The Last Stand: Magneto is "cured" from his mutation. Subverted in that the cure seems to be temporary.
Kick the Dog: Mystique shields Magneto from being shot with a cure-gun by Taking the Bullet herself. Magneto abandons her because she's "no longer one of us." He does at least seem sad while he does it...
Magic Pants: Wolverine survives the telekinetic disintegration due to his healing factor. How his pants also survive...
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.
The Other Darrin: Hank McCoy/Beast had a small cameo in X2. Granted, he hadn't mutated yet, but the actor still looked and sounded nothing like Kelsey Grammer.
The Stinger: Professor X transfers his mind into the man with the coma...
Twist Ending: Magneto slightly moves a chess piece. Maybe his powers are returning.
An unused one would have had Mystique sitting next to him, revealing that the two had been in league the entire time. Unfortunately, the actress wasn't available.
What Could Have Been: Summer Glau auditioned for the role of Kitty Pryde (using Joss Whedon's Astonishing X-Men No. 5 as her audition material!). The fandom would have rejoiced.
David Hayter briefly mused about adapting the Dark Phoenix Saga on the commentary track of an earlier X-Men film. He mentioned the idea for Jean to commit suicide by telekinetically forcing Scott to look at her without the visor. Sadly, Hayter was not involved with the third film.
Will They or Won't They?: Iceman and Rogue. Iceman seems disappointed that Rogue "cured" herself, even though she did it for both of them. Its unknown what their relationship is now, especially since the cure is temporary.
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