In the show, Wolverine attempts to reassemble the X-Men and becomes their new leader, following a devastating incident that led to the disappearances of both Jean Grey and Charles Xavier.

Due to the loss of the Professor, Jean, and severe damage to the mansion, many of the X-Men have withered in their faith towards the stability of their former team and have since detached themselves from their former community.

Thanks to the generosity, wealth, and resourcefulness of Angel, the X-Men team begins to return to its former glory with the rejoining of junior members Iceman, Shadowcat and Forge along with the reconstruction of the Xavier Institute.

Unfortunately, without the necessary capabilities of a competent telepath to operate Cerebro, the possibility of locating some of the more globally scattered X-Men members along with the missing Charles Xavier and Jean seems all but a pipe dream.

Fortunately, this problem does not last for very long when Emma Frost, the headmistress of a now inactive mutant school of her own in Massachusetts, makes a surprising appearance on the doorstep of the Mansion with an interesting proposal: membership with the X-Men in exchange for utilizing her telepathy to pinpoint the missing Xavier's whereabouts.

Upon the team's – and particularly Wolverine's – reluctant acceptance of the offer, Emma's efforts prove successful as she is able to locate a comatose Charles on the shores of Genosha in the care of Magneto.

After their arrival on Genosham Magneto permits the X-Men to take his old friend's body back to the sanctity of the Mansion where he is certain that Xavier will be placed in proper care.

Throughout the course of the entire season, Emma's role as the X-Men's primary acting telepath enables the team to relocate the rest of the other members in the hopes of reforming once again and assisting in Xavier's cause.

While some were met with initial hesitancy such as with Nightcrawler, others such as Storm were more than willing to accept the offer once Xavier's vision had been put into perspective.

It is later revealed in the three-part first-season finale "Foresight" that the previously assumed attack on the Mansion was not from the efforts of a third party, but rather from the result of Jean who unwittingly releases the Phoenix Force, that originally lay dormant within her mind, in an attempt to halt an oncoming telepathic attack led by Emma (who was working as a double agent for the Inner Circle and the Stepford Cuckoos).

Along with Sebastian Shaw, Selene, Harry Leland, and Donald Pierce, it was the Inner Circle's utmost duty to not only obtain the power of the Phoenix Force by abducting Jean from the protection of Xavier and the Mansion, but to also obliterate the ancient being's existence before it could fully mature and consequently bring forth unparalleled destruction onto the world as it had done numerous times in the past throughout Earth's history.

However, in a move that was completely unknown to Emma at the time, the rest of the Inner Circle members sought to manipulate the Phoenix Force and cater to their own agenda.

The now fully reformed X-Men are praised for their actions by Professor Xavier, but are warned of a new danger approaching: the Age of Apocalypse.

While Professor X is in his mansion, the final shot shows a high-tech pyramid as Apocalypse, Mister Sinister, and Cyclops are about to address a crowd.

Beast and Wolverine manage to bring Shadowcat and Iceman back the X-Men, while some such as Cyclops, Colossus, and Rogue, do not wish to return.

Meanwhile, Nightcrawler and the other travellers (including Squid-Boy, Vindaloo, Network, Shatter, Pixie, Feral, and other mutants) are intercepted by "pirates", who really are Spiral and the Reavers, looking for fighters to take to Mojo.

Nick Fury asks Wolverine a "favor" to once again fight against the Hulk in exchange for keeping the X-Men's identities and the Xavier Institute secret.

Meanwhile, the X-Men fight the Brotherhood and find Tildie Soames (a young mutant whose nightmares can manifest into monsters) is attacking the city while still in a coma-like state.

An amnesic Jean uses her incredibly strong and powerful telepathic and telekinetic abilities while at the hospital, which allows Emma to locate her using Cerebro.

Meanwhile, Magneto hatches a plot against the human race, having replaced Senator Kelly with Mystique to start an attack on Genosha.

Emma discovers the Hellfire Club's true motivation for using the Phoenix Force, and fights to free Jean alongside Cyclops.

Accordingly, Magneto reprograms the Sentinels to attack humans with help from Mystique posing as Senator Kelly who is imprisoned in Genosha.

[22] During Comic Con 2009, images of season 2 were shown, consisting of Bastion, Cable, Colossus, Deadpool, Havok, Jubilee, and Magik.

[25] On April 15, 2010, Marvel Animation Age confirmed the recent report that Wolverine and the X-Men would not be returning for a second season.

[28][29] It was also confirmed in an article by USA Today's website in which it specifically mentions the cartoon starting on January 23, 2009, on Nicktoons Network.

[30] On January 23, 2009, the show premiered in the United States, with the first two episodes shown back-to-back on Nicktoons Network, which were re-aired on Nickelodeon two days later.

On June 23, 2008, a second preview for the series, starring the main X-Men team, was released to announce the special screening of the 3-part pilot episodes that aired at San Diego Comic-Con in late July 2008.

CBBC in the UK overtook Canada on March 4, 2009, when it aired the 20th episode, "Breakdown.” In 2009, BBC Alba started broadcasting the series dubbed into Scottish Gaelic as "An Sionnach Sgianach is Na Seòid".

The first wave consisted of Avalanche, Beast, Colossus, Cyclops, Logan (not in classic outfit), Iceman, Magneto, and Wolverine.

Magna Home Entertainment has announced that the full first season (26 episodes) has been released in Australia with a Limited Edition Wolverine Mold Case.