The second movie in the X-Men series involves mutants who are being mind-controlled somehow, starting with Nightcrawler attempting to assassinate the President; government operatives then kidnap Cyclops and Professor X. The X-Men investigate and find out that the two are related: the soldiers are under the command of Col. William Stryker (Brian Cox), who is using a mutant to project false images into other mutants' minds. By brain-washing Professor X into overpowering the "Cerebro" telepathy machine, he intends to kill all currently-living mutants. Magneto and his Brotherhood Of Mutants ally with the X-Men to stop this from happening (hence the subtitle of the movie: "X2: X-Men United"). Meanwhile, Wolverine delves into his past involvement with the "Weapon X" project, which (of course) Stryker was in charge of.Not to be confused with the series of sci-fi videogames by the name X, whose second entry is entitled X2.
This film provides examples of:
Aerial Canyon Chase: Lacking a conveniently placed canyon with which to perform this, Storm uses her weather manipulating powers to create one from tornadoes, giving the X-Men a chance to escape. It has the added benefit of making sure the inevitable crashes aren't actually fatal for their pursuers, but also the downside of allowing a clean missile lock.
Alas, Poor Villain: Lady Deathstrike, who was only being mind-controlled. Even the look on Wolverine's face shows he regrets that he had to do it.
And I Must Scream: Stryker's mind control serum makes the victim obedient, but their real self is still in there, fully aware and incapable of controlling their own body. Look at the sheer horror on Deathstryke's face when the serum controlling her briefly wears off. Particularly when she looks at her hands and remembers the pain of being bonded with adamantium, likely because she was being controlled during that, as well. Scott similarly tells Jean he couldn't stop himself from trying to kill her.
Asshole Victim: Mitchell Laurio. He's a thug who's shown to enjoy beating up an old man stripped of any powers that would allow him to fight back, so no one minds too much when Mystique sets him up for a death allowing Magneto to escape.
Bait the Dog: Just when you're starting to cheer on Magneto as he charges alongside the X-Men to Xavier's rescue, he has to go and use Xavier to try to wipe out every normal human.
Best Her to Bed Her: Mystique tries to seduce Logan/Wolverine in this film because he defeated her in combat in the previous one, complimenting him that "nobody ever left quite a scar like you did". Logan is not interested. Later films show that Mystique is capable of having loving, if not necessarily intimate, relationships with other mutants even if they didn't actually beat her (Charles Xavier, Magneto).
Big Damn Heroes: Magneto, of all people - when the Blackbird is about to crash into the forest.
Blessed with Suck: Jones, one of many of the Xavier Institute's students. He can change television channels by blinking, but he never sleeps.
Brainwashed and Crazy: Various mutants (including Nightcrawler, Cyclops and Deathstryke), by Stryker. Also Xavier, by Stryker's mutant son Jason, who is himself Lobotomized and Crazy.
Call Back: When the mutants are flying to Alkali Lake, Magneto and Mystique sarcastically say that they like the white parts of Rogue's hair. Those parts were turned white by Magneto's machine during the climax of the first X-Men movie.
Can't Have Sex, Ever: Multiple characters point out the inherent problems faced by Iceman and Rogue.
Creator Cameo: The security guards for Magneto's prison are all named after production staff. Director Bryan Singer gets his own pic, uniform and all, while the rest are given stock male photos.
Dangerously Genre Savvy: Stryker takes one look at Wolverine, and realizes it's a fake. Also, at one point he tells his men to shoot anyone who comes down their corridor, then adds "even if it's me", fully aware that the enemy has a shapeshifter among them.
The Dog Bites Back: Magneto to Stryker when he finally gets a chance to get some payback for his treatment in prison. An earlier script was going to have Magneto kill Stryker (which would be more in character) and the X-Men find Stryker's body when they escaped from the facility - but that was changed for the sake of letting Wolverine have one last conversation with Stryker.
Evil All Along: Magneto, who, right after saving the mutants of the world, can't resist seizing the opportunity to use Stryker's technique against humanity.
Evil Cripple: Jason Stryker, provided his father was telling the truth about him deliberately driving his mother to suicide, and that wasn't just Jason being unable to control his powers or unaware of what he was doing.
Finger Snap Lighter: Averted with John/Pyro, who carries around an actual lighter since he can't generate fire on his own.
Foreshadowing: When Professor X is having difficulty trying to get a lock on Nightcrawler, Logan flippantly asks if he can't just concentrate harder. Xavier replies dryly, "If I wanted to kill him, yes." Later Stryker gets Jason to brainwash Xavier into doing precisely this - only on a much larger scale.
Freeze-Frame Bonus: William Stryker's computer desktop is a treasure trove of shout outs. You'll see folders marked things like 'Victor Creed', 'Omega Red', 'Maximoff (2)', 'Project: Wideawake', 'Franklin Richards', and so many more!
Likewise, Stryker isn't fooled when Mystique masquerades as Wolverine. One thing he knows better than anyone is his own work.
A Glitch in the Matrix: During Jason Styker's initial attempt to trap Xavier within an illusion of the mansion, it doesn't work because Xavier notices that he's standing up. Jason's next attempt has him sitting in a wheelchair.
Handy Cuffs: On Mystique; not that handcuffs of any type would have been useful on a shapeshifter. She was disguised as Wolverine at the time, and the cuffs would have worked very well on him, being designed in such a way that if he extended his claws he'd cut off his own head.
Hijacked by Ganon: Magneto works with the X-Men without much protest or animosity to save mutant-kind, but once he foils Stryker's plan he reminds us that he is the Big Bad of the series and turns Strkyer's Cerebro on normal humans.
Hoist by His Own Petard: Stryker's mutant-killing machine is ultimately turned on humans instead, which naturally includes Stryker himself. It gets shut off before it can do the job, of course, but it was long enough to make sure Stryker never escaped.
Idiot Ball: The entire broken dam scene. Iceman and Storm could have conceivably saved the day without needing a Heroic Sacrifice, since both are capable of manipulating the temperature of water. Likewise, Jean's actions could have easily been done from the safety of the plane. The characters come to the conclusion that Jean did it deliberately, rather than a mere lack of forethought.
Rogue attempting to fly the Jet, without any training in its operation, simply because she was getting impatient. It predictably crashes only a few seconds after take-off and ends up being damaged, forcing Jean to sacrifice herself.
Earlier, Xavier has a minor but understandable one. He notices that Deathstryke is starting to regain control. He's smart enough not to say anything, but the fact that he keeps glancing over to her alerts Strkyer, allowing him to give her another dose of serum to keep her obedient.
Instant Sedation: Stryker's tranq darts. All the kids hit by them go down in a snap. Cyclops was protected by the armor under his clothing and Wolverine is understandably immune (but momentarily dazed, regardless). Mystique's drugged beer also takes effect the second Mr. Laurio downs the last of it, where the pills have settled.
Jerkass: Ronnie, Bobbie's brother, calls the cops on Bobbie and his friends under the pretense that they were holding his family hostage.
Likewise Pyro, who, swayed by Magneto's words, starts falling into the dark side. Even escalating the whole situation with the police by openly attacking them when the others were trying to halt the situation peacefully.
Market-Based Title: The film's simply called X-Men 2 in the UK, France, Brazil, Finland and several other countries.
Martyr Without a Cause: Jean Grey, who sacrifices herself while holding back a giant wall of water to allow the rest of the team time to escape. There were at least three other team members (Storm, Iceman, and Nightcrawler) with powers that would have been useful in this situation, and with all four of them working together, they at least stood a chance of getting everyone out alive. She never gave them the chance to try.
Mundane Utility: When Logan wants a cold drink, he gives a Dr Pepper to Bobby "Iceman", who uses his powers to chill the drink.
Mythology Gag: After Magneto saves the Blackbird, he says "When will these people learn to fly?", referencing the fact that several of the X-Men can fly in the comics.
No Sell: Xavier is, understandably, immune to just about every telepathic attack imaginable. Now, if he were under the effects of a Power Nullifier and bombarded with illusions for two days straight...
Nice Job Breaking It, Hero: Rogue's impatience makes her indirectly responsible for Jean's death, due to crashing the Jet and causing the vertical takeoff to go temporarily offline. Furthermore, since the Jet appears to have been only about a few hundred metres from the facility, she really didn't need to fly to pick them up anyway.
Party Scattering: Prof. X and Cyclops are captured at the same time but taken to different areas where different things happen to them. Storm and Jean go after Nightcrawler and eventually run into Magneto. The government kidnaps several mutants and take them to their facility. Wolverine and a few of the students escape the mansion and hide out at Iceman's house for a while. They come back in the third act.
Psychic Radar: It's already been seen in the previous film that Cerebro amplifies Xavier's powers to give him greater range and accuracy. Here he uses it to allow him to track even a mutant who can teleport and it's further revealed that he can use it to sense the location of every mutant or every human on the planet. Concentrating hard enough will give them all a really serious Psychic Nosebleed... followed by death.
Psychotic Wink: Magneto performs one after admonishing the (dead) guard for unwittingly aiding in his escape.
Shooting Superman: After using their tranq darts on some of the students, two of Stryker's men are confronted by Colossus. The big guy activates his power, but the agents try firing anyway. After the darts bounce off of him, Colossus throws the agents through a wall.
Slipping a Mickey: Mystique slips a drug into Magneto's guard's drink in order to knock him out so she could inject enough metal in his body for Magneto to sense and manipulate to break out of prison.
Standard Snippet: Mozart's Dies Irae plays during the opening scene where Nightcrawler is bamfing through the White House, and it's arguably the most memorable music moment in the entire series.
The Stool Pigeon: Magneto was a Lacerated Larry in the beginning: It is strongly implied that Stryker had arrived at Magneto's cell beforehand and injected him with the same brainwashing serum from his son to get him to lure Professor X into his prison so X could be captured.
Teleport Spam: Nightcrawler's attack on the White House, where he's kicking, throwing, punching, and just beating the crap out of every agent from every angle, with the last one in glorious slow motion.
Throwing Out The Script: The President discusses his speech as he walks down a hall with some staffers, then his speech is in the teleprompter, and he's going live when Professor X and the rest of the X-Men pay him a visit and provide him with documents from Col. Stryker's office. The X-Men leave, time resumes for the staffers, and the POTUS touches the file on his desk and begins to improvise...
Too Dumb to Live: So, you have a school for the members of a severely hated group, and this school possesses very advanced technology. Why on earth do you not have a security system? I mean, even if you don't do anything to stop invaders from just climbing over the wall and jumping through the windows, at least have an alarm so they don't catch half of everyone asleep!
Viewers Are Morons: Originally, Xavier's hallucination of him returning to the mansion was much more convincing, with scenes of him teaming up with Jason to free Scott and hypnotizing a guard into helping them escape via a helicopter. The problem was, the screening audiences mistook the hallucination for the reality of the movie and were confused by how later scenes conflicted with that.
What Could Have Been: Originally, Ray Park was to return as Toad and get into a fight with Nightcrawler; however, schedule conflicts prevented this.
While You Were in Diapers: Stryker to Kelly. Both in-universe and out this just sounds ridiculous, as Stryker can't be that much older than Kelly, not to mention that Brian Cox is actually only about three weeks older than Bruce Davison (who admittedly doesn't look his age at all).
Window Love: Wolverine and Stryker, through a wall of ice.
You Are Number Six: General Stryker had his son Jason lobotomized after lashing out against him and his wife. Since then, the General simply refers to him as "Mutant 143". When Professor X expresses his shock over it, asking why he'd do this to his own son, Stryker simply answers with: "No, Charles. My son is dead. Just like the rest of you."