[1] Taking inspiration from the early issues of the original comics, the series portrays the X-Men as teenagers rather than adults, following their struggle to control their mutant powers as they face various threats.

The titular team, founded by Professor Charles Xavier, competes with Mystique to recruit young mutants with newly discovered superpowers to their cause.

[3] Their ranks grow over the course of the season and ultimately include Cyclops, Jean Grey, Nightcrawler, Shadowcat, Spyke, and Rogue, who is initially manipulated into joining Mystique's Brotherhood of Bayville.

While the X-Men teach their recruits to exercise restraint and uphold responsibility, Mystique encourages the Brotherhood to recklessly use their powers for selfish gain.

The mastermind behind Mystique and the Brotherhood is eventually revealed to be Magneto, a shadowy and mysterious figure from Xavier's past who seeks to enable mutants to replace humans as the dominant species on the planet.

The X-Men are faced with several threats: Mystique strikes off with the Brotherhood and recruits the Scarlet Witch, Magneto's abandoned daughter and Quicksilver's sister, to seek revenge; Mesmero plots to free the ancient mutant Apocalypse; and Magneto forms a new group of mutant followers called the Acolytes, comprising Sabretooth, Gambit, Pyro, and Colossus.

The existence of mutants is ultimately revealed to the world when Magneto pits the X-Men and the Brotherhood against Bolivar Trask's anti-mutant weapon, the Sentinel.

After Xavier is found and rescued, the X-Men attempt to rebuild their normal lives in Bayville and continue using their powers for good, though they face public scrutiny and discrimination from the other students at school.

The X-Men are forced to contend with numerous personal struggles: Cyclops is abducted and left for dead by Mystique; Spyke leaves the team to join the sewer-dwelling Morlocks when his mutation rapidly advances; Nightcrawler overcomes his insecurities about his appearance; Rogue learns that Mystique is her adoptive mother and loses control of her powers; and Wolverine discovers that he has a teenage clone called X-23, who was created by HYDRA to be trained and used as a weapon.

Meanwhile, Magneto enlists Mastermind to alter Scarlet Witch's memories to end her vendetta against him; and Mesmero manipulates Mystique and hypnotizes Rogue into helping him resurrect Apocalypse, who defeats the combined forces of the X-Men, the Brotherhood, and the Acolytes.

The Brotherhood try their hand at heroism, only for their selfish tendencies to prevail; Wolverine and X-23 work together to bring down HYDRA; Xavier confronts his estranged son David; Spyke and the Morlocks begin fighting back against human prejudice; Shadowcat befriends Danielle Moonstar; and Rogue pushes Mystique's petrified statue off a cliff, creating a rift between her and Nightcrawler, which causes her to seek redemption by helping Gambit to rescue his father.

Apocalypse captures and transforms Xavier, Storm, Magneto, and Mystique into his Four Horsemen as he attempts to turn the human population into mutants.

During the final battle, the X-Men and their allies defeat the Horsemen, who are returned to normal, while Rogue absorbs the powers of Dorian Leach to neutralize Apocalypse and trap him in his tomb forever.

In the aftermath, Rogue and Nightcrawler rebuff Mystique's attempt to make amends; Magneto reconciles with Quicksilver and Scarlet Witch; Shadowcat and Avalanche rekindle their relationship; Spyke reconnects with his aunt Storm; and Xavier sees his students reunited as the X-Men.

These include Jean Grey (light chime noise), Sabretooth (roaring), Rogue (also has a unique, black and white special effect), Magneto, Gambit, Shadowcat, and Nightcrawler.

Using Shadowcat as the catalyst, the two shows appear similar: a teenage girl with superpowers fights powerful villains in order to save her high school.

It was not a continuation of X-Men: Evolution, though the same creative team was behind the show: Craig Kyle, Chris Yost, Steven E. Gordon, Greg Johnson and Boyd Kirkland all returned to work on the series.

In 2012, Jean Grey and Robert Kelly (voiced by their respective X-Men: Evolution actors) appeared in the Iron Man: Armored Adventures episode "The X-Factor".

Choi acknowledged that "The students generally have abilities more powerful than they ever had in the comics," specifically mentioning intangible Shadowcat and telekinetic Jean Grey.

While praising the show's animation and music – "cleaner than the original series" – Choi described the transformation of Rogue "into a reclusive goth chick" as " completely baffling but surprisingly palatable.

"[12] Noting the show's treatment of its characters, specifically making them high school teenagers for thematic purposes as "admirable," John G. Nettles of PopMatters concluded, "What disappoints, however, is the sheer number of missed opportunities here and the decision to subscribe to the same old social norms.

He also noted that combined with "inventive gags," "the show does its best to make the most of the mutants' powers" because "The fight scenes are fun to watch if only to see how the characters interact.

The series' bible was written by Robert N. Skir and Marty Isenberg (albeit uncredited), who meant to take The X-Men back to their roots as high school students learning to control their superpowers, as when the comics termed them "The Strangest Teens of All".

In "Day of Recovery", Toad is seen to be quite comfortable with technology and in "Operation Rebirth", the POW camp Magneto is held in as a child is visually similar (in the opening shot) to Auschwitz, though it is not identified as such.

Aside from this, supporting characters like Bolivar Trask, Nick Fury, Captain America, Destiny, Agatha Harkness and Amanda Sefton were all taken from the X-Men comic, usually serving to homage to originals without necessarily staying completely faithful to their form.

X-23, an original character introduced in later seasons,[19] made her comic book debut in the miniseries NYX,[20] where her appearance was slightly altered to more closely resemble Wolverine.

One of the masks worn by the vandals in the Season 3 episode "Mainstream", bears a suitable resemblance to the classic Marvel Comics monster, Fin Fang Foom.

Also in "Dark Horizons Part 2", Nightcrawler, Colossus, and Shadowcat are grouped together when the X-Men and the Acolytes are separated, a reference to the Europe-based superhero team Excalibur which included all three mutants in its roster.

Written by Devin K. Grayson with art by Studio XD, it was abruptly canceled after the ninth issue due to low sales.