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The series was a retitling of the then-ongoing second volume of the X-Men series which began in the early 90's, and shared the series' numbering. Morrison, a critically-acclaimed writer known for his high-profile works at DC Comics, was brought onboard to revitalize the title and introduce a number of new story elements. The series started with a shocking development, as the new villain Cassandra Nova directed an army of Sentinels to destroy the mutant island Genosha, resulting in millions of deaths and a shake-up to the status quo.
The following arcs introduced several new students at Charles Xavier's school (including Beak, a deformed half-human birdman, Angel Salvadore, a young woman who sports the wings of a fly, the Stepford Cuckoos, and Xorn, a Chinese prisoner who can heal injured people and sports a black hole inside his helmet), and dealt with more mature themes. The series culminated in a storyline, "Planet X", that was over two years in the making - Xorn revealed himself to be Magneto (who was thought dead after Genosha was destroyed), and subsequently crippled Xavier while enacting a plan to turn Earth into a mutant haven and exterminate humanity in the process.
The series comprised nine story arcs (and one annual issue), including:
- E For Extinction (#114-116): Cassandra Nova makes her first appearance and uses an army of Sentinels to destroy Genosha, Emma Frost rejoins the team and Xavier (possessed by Nova) outs himself as a mutant on live television.
- The Man From Room X (Annual 2001): The team travels to Hong Kong to rescue a captive mutant named Xorn, who has many dark secrets, and is persuaded to join the team.
- Imperial (#118-126): Several new students are introduced at the Xavier Institute, while the team goes into Xavier's mind to free him from Nova's influence. Meanwhile, Nova uses Xavier's powers to manipulate the Shi'ar into attacking the Xavier Institute.
- New Worlds (#127-133): The team revisits Genosha to look for survivors, as well as broker peace amidst rising mutant/human tensions, while Cyclops begins a "psychic" relationship with Emma.
- Riot At Xavier's (#135-138): One of Xavier's students, Quentin Quire, begins to mock his mentor's pacifistic teachings, and (along with a group of militant classmates, all hopped up on the mutant drug Kick) attempts to kill humans and cause a riot in retaliation.
- Murder At The Mansion (#139-141): After discovering Scott's psychic relationship with Emma, Jean freaks out and uses the power of the Phoenix to burn through the White Queen's defenses. Later on, Emma is found to have been shattered into thousands of pieces, prompting an investigation into what caused her death.
- Assault On Weapon Plus (#142-145): Fantomex, Cyclops and Wolverine journey to a dormant asteroid that houses the remnants of the Weapon Plus program, which is discovered to go back to at least World War II, and results in Wolverine discovering his past.
- Planet X (#146-150): The series climaxes with Xorn revealing himself to be Magneto and throwing the entire Xavier Institute into chaos when he cripples Xavier again and attempts to exterminate humanity as a precursor to turning Earth into a mutant haven.
- Here Comes Tomorrow (#151-154): The final arc written by Morrison, which follows a group of mutants in the far future who discover Jean Grey inside a Phoenix Egg and attempt to free her, while Beast (under the influence of Sublime) attempts to destroy the X-Men once and for all.
- Bright New Mourning (#155-156): The only New X-Men arc not written by Morrison (Chuck Austen took over writing duties). The story was a bridge to the "Reloaded" series (which went back to the traditional X-Men title), and followed the team as they rebuild after the events of the "Planet X" arc.
The book resulted in a re-energizing of the franchise, and was critically and commercially acclaimed. However, the revelation that Xorn was actually Magneto in disguise was hastily retconned by Marvel after the run due to fan backlash. The series reverted back to the original X-Men title beginning at issue #157.
For the series New X-Men: Academy X, visit the New Mutants page.
The series contains examples of:
- Alternate Universe: "Here Comes Tomorrow".
- Apocalypse How: Magneto's plan in "Planet X" is a Class 4 (species extinction) - he intends to repopulate Earth with mutants.
- Back From the Dead: Jean/Phoenix and Magneto during the "Planet X" storyline.
- Badass Longcoat: Fantomex.
- Bad Future: "Here Comes Tomorrow" - most of the X-Men (and humanity) are dead, with the few survivors being Fantomex's A.I. EVA, the Stepford Cuckoos and Wolverine.
- Bare Your Midriff: Emma and Jean.
- Betty and Veronica: Jean and Emma to Scott. Resolved at the end of the series when Jean uses the Phoenix Force to convince Scott to let her go and be with Emma.
- Berserk Button: Jean's death does this to Wolverine, who promptly decapitates Xorn/Magneto.
- Big Bad: Cassandra Nova, Quentin Quire, Xorn and alternate-universe Beast.
- Big Damn Heroes: The Stepford Cuckoos take it upon themselves to stop Quentin Quire's riot. Sophie uses Cerbra (and some Kick) to boost their abilities while her sisters handle Quentin face-to-face. Sophie dies as a result, though this turned out to be orchestrated Esme.
- Bigger Bad: Sublime. He was behind everything from the Kick drug to the creation of Weapon X (actually the tenth experiment of Weapon Plus), and may even have manipulated humanity into turning against mutants in the first place.
- Birds of a Feather: Beak and Angel, who come from similar backgrounds and meet when a group of students dares Angel to kiss the ugliest student in the school. They eventually raise a family together.
- Black Bug Room: The Trope Namer. Cyclops is sent there by Cassandra in issue #116.
- Blessed with Suck: Angel Salvadore has the ability to fly, but does so at the cost of not being able to consume her food properly (she has to vomit on it and digest it like paste).
- Brainwashed and Crazy: Xavier after Cassandra takes over his mind, and Beast in "Here Comes Tomorrow".
- Breather Episode: "Assault on Weapon Plus". After all of the drama over Scott's infidelity and the attempt on Emma's life, Scott goes out for a nice "boy's night out" with Logan and Fantomex (which involves them battling some cyborgs and breaking into a space station). They get back just in time for "Planet X".
- Call Back: Just before Jean dies, she makes reference to dying right after coming back as the Phoenix.
- The Cameo: Though mostly absent, a few of the X-Men outside of the main five make brief appearances. Archangel appears after "Imperial" to give a few of the new students a flying lesson. Storm can be seen helping with the cleanup of Genosha.
- In addition, some of the auxiliary X-teams also appear as employees of the X-Corporation--many of the members of X-Factor work for the Paris branch, and a few former X-Force members work for the Mumbai branch.
- Civvie Spandex: The team (sans Emma) wears matching yellow-and-black leather jackets and pants for the duration of the series.
- Composite Character: Sort of. Morrison says that he gave Emma the ability to turn into diamond because he originally wanted to put Colossus in the team's lineup, but decided to combine his powers with another character after he was killed off in the "Legacy Virus" arc.
- Darker and Edgier
- Darkest Hour: Issue #147 - Xavier has been crippled (again), Xorn has revealed himself to be Magneto and leaves with several of Xavier's students, Logan and Jean are on an asteroid that's hurtling into the sun, Hank and Emma are stuck on a small island in the middle of nowhere after the Blackbird crashes, and the rest of the team is scattered and unsure of what to do.
- Deadpan Snarker: Jean Gray as Phoenix, who starts by passively asking the mutilated Wolverine if his "eyes have grown back yet" and dies just after she remarks to Cyclops how she seems to come back only to die again soon after.
- Deconstruction: The series explores many of the harsher aspects of how an oppressed minority of superhumans might function in the real world, with abuse of power-enhancing drugs, campus insurrection at the Xavier Institute, the homegrown culture of the "mutant ghetto", and even Che Guevara-esque idolization of Magneto figuring into the plot.
- Decon Recon Switch: Joss Whedon's Astonishing X-Men (New X-Men's direct sequel) continued most of the series' themes and plot arcs while recasting the X-Men as traditional superheroes, complete with their classic spandex costumes. Though every bit as dark and mature as Morrison's run, it managed to reconstruct the action and adventure of the Claremont era, showing that there's still a place for superheroics amidst the chaos and ambiguity of the modern world.
- Dropped a Bridge on Him: Genosha is unceremoniously destroyed at the end of the first issue of "E For Extinction", killing millions and leaving a few survivors to pick up the pieces. By the end of the "Planet X" arc, Jean is also dead.
- Drugs Are Bad: Both Quentin Quire and Xorn/Magneto are revealed to be addicted to the mutant drug Kick, which enhances their powers and motivates the "Riot At Xavier" and "Planet X" arcs.
- Easily Forgiven: The rest of the team doesn't seem to bear Emma any ill will for seducing Scott behind Jean's back. Even Professor Xavier, who has very little tolerance for people using psychic powers to manipulate others, doesn't call her out on her using telepathy to exploit his confusion.
- Evil Twin: Cassandra Nova is Charles's twin sister, whom he killed in the womb to self-defense. Esme Cuckoo is a subversion, as she's an Evil Quintuplet.
- Face Heel Turn: Esme Cuckoo, who gets hooked on Kick, tries to murder Emma, and finally falls in with Magneto when he tries to destroy New York City.
- Fan Disservice: Jean, who previously stripped down to her bra and pants while on Asteroid M as it's hurtling into the sun, is stabbed in the gut by Logan.
- Five-Man Band:
- Future Badass: Beak's grandson Tito Bohusk Jr., who is essentially Beak with full control over his flight powers--and without the angst or social awkwardness.
- Gentleman Thief: Fantomex.
- Great Offscreen War: Sublime's takeover of Earth happens completely offscreen. After "Planet X", the action cuts straight from the present day to 150 years in the future.
- Heel Face Revolving Door: Beak, who ends up joining Xorn/Magneto when he reformed the Brotherhood of Mutants, then regained his conscience and rejoined the X-Men as they made their assault on the Brotherhood's base.
- Heroic BSOD: Polaris is revealed to have been in this state for months when the team finds her on Genosha - she blamed herself for not being able to save the millions of massacred mutants, and became a nude, deranged recluse who wandered around the island.
- Kill'Em All: The ending of the "Here Comes Tomorrow" arc.
- The Lancer: Fantomex is this to Wolverine over the course of the series. In hindsight, it makes more sense - Fantomex is a later participant of the Weapon Plus program.
- Loads and Loads of Characters: While none of them receive that much panel time, the Xavier Institute was filled with hundreds of students each with unique mutations. Most of them weren't properly identified until years later.
- Man in White: Fantomex.
- Meta Origin: The series officially canonizes the fact that mutants can receive additional secondary mutations, highlighted by Emma's survival during the destruction of Genosha (she becomes an indestructible diamond form, at the cost of the temporary loss of her telepathy).
- The Weapon X program also gets this treatment. We learn that the "X" in its name is actually the Roman numeral for "10"--it's the tenth in a series of experiments devised by Sublime to create the perfect super-soldiers for combatting the mutant menace. The project began with in World War II with the creation of Weapon I...better known as Captain America.
- Ms. Fanservice: Emma, natch.
- Neck Snap: Emma does this to Cassandra at the end of the E For Extinction arc.
- New Powers as the Plot Demands: Morrison's run introduced the concept of "secondary mutations", with a few of the X-Men gaining new powers. Conveniently, Emma discovers her ability to transform into diamond right after a building falls on her.
- Not Using the S Word: Morrison wanted to distance X-Men from its roots as a superhero comic in favor of making it a more nuanced, realistic science-fiction comic--so the characters almost never use the word "superhero", aside from a scene in the first issue where Beast tells Professor Xavier "I was never sure why you had us dress like superheroes" when reviewing the new uniforms.
- Party Scattering: Done intentionally by Xorn/Magneto to separate the team while he cripples Xavier in "Planet X".
- Psychic Link: The Stepford Cuckoos.
- Puberty Superpower: Both Beak and Angel manifested their powers when they were in their teens - Angel was thrown out of her home when her father discovered she could fly, and Beak fled his home after discovering his physical changes.
- The Real Remington Steele: Xorn, who "reveals" himself as Magneto before being killed.
- Remember the New Guy?: Cassandra (Xavier's "twin" sister), who appears at the beginning of the series.
- Rewrite: The Weapon X facility is explained to be just one of several such installations created throughout the world. Captain America is revealed to be "Weapon I" (from the Project: Rebirth program), while several other characters (including the Stepford Cuckoos) are revealed to be later test subjects.
- Roaring Rampage of Revenge: Emma in the "E For Extinction" arc, who initially goes after humanity for destroying Genosha, but discovers the real culprit (Cassandra) and snaps her neck.
- Robot Buddy: Rover in "Here Comes Tomorrow" is a sentient, slightly dimwitted Sentinel (one of the few still left on the planet) who is commanded by future X-Man Tom Skylark.
- The Runaway: Beak and Angel.
- Single Woman Seeks Good Man: Emma, to Scott.
- So Proud of You: Inverted. After Emma kills Esme, she cradles the dying girl and tells her that in spite of her turning against the X-Men, she's still proud of her.
- Space Whale Aesop: "Here Comes Tomorrow" - Humanity and mutantkind are doomed unless a man who just lost his wife immediately begins sleeping with another woman.
- Stripperific: Emma - this is highlighted by the final issue (#156), which has a cover photo of her (wearing a skintight pantsuit) hugging Cyclops while looking devilishly into the camera as she sticks her back out.
- Superior Species: Xorn/Magneto uses this as his excuse to exterminate humanity and make Earth into a haven for mutants.
- Superman Stays Out of Gotham: Partially averted. Magneto says that he tricked the Avengers and Fantastic Four into going on a wild goose chase while he enacts his plan to exterminate the humans, but this doesn't explain why any of the myriad superheroes/superhero groups in the city don't do anything to help. There's no way Spider-Man, Daredevil or Luke Cage would have stood by while people were herded into gas chambers.
- This is actually handwaved by Beak, who mentions that Magneto was keeping the other heroes busy with a false threat concerning a "black hole bomb" in Brooklyn.
- There Are No Therapists: Averted - Emma takes over as the school's resident teacher/therapist, and ends up counseling many of the students.
- Unresolved Sexual Tension: Comes back when Logan and Jean are stranded on Asteroid M together.
- Utopia Justifies the Means: In issue #150 (the final part of "Planet X"):
Magneto: May the future forgive me. May history judge my actions, great or small. In the final reckoning... when I have given them paradise, and the world is free... those poor dead will not seem so many. Now, let the sky fall.
- Was It All a Lie?: Esme's boyfriend Kato turned out to be a shapeshifting member of the Imperial Guard, Stuff. A shocked Esme mentions that "Kato" read her poetry and told her he loved her, to which Stuff coldly replies "and like a fool you believed me."
- Wham! Episode: The "Planet X" arc is a concentrated sequence of these - Xorn reveals that he's Magneto, Jean finds Logan alive and well at the asteroid, the asteroid is destroyed and Jean becomes the Phoenix again, Xavier is crippled (again), Magneto enacts his plan to kill all the humans in New York and many mutants are killed, including Magneto, Esme (one of the Stepford Cuckoos) and Jean, just before the last panel reveals that the Phoenix Force is alive and well hundreds of years in the future!
- Whole-Plot Reference: The "Here Comes Tomorrow" arc is heavily influenced by The Wizard of Oz. Many of the characters are direct copies of those found in Oz (Tom and Rover are Dorothy and Toto, flying Nightcrawlers are the flying monkeys, Tito is the Cowardly Lion, etc.), and the ending strongly mirrors the film (someone wishes for something to be true, and goes to a wizard for help).
- Wolverine Publicity: Lampshaded - one of the students asks how Logan finds the time to be on three teams at once.
- Younger Than They Look: Ernst is a little girl with super strength, but her mutation has made her look like a little old woman.