10 Best X-Men Stories of the ‘00s

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In the ’90s, the Uncanny X-Men, X-Men, Wolverine, and occasionally X-Force were consistently among the top ten bestselling comic books. However, one of the challenges facing the comic book industry during this time was the overwhelming popularity of the X-Men, as well as the repetitive nature of their stories. Sales were dwindling across the board, and readers seemed to be growing tired of the same narratives. Change was needed, and it came in the ’00s. Marvel Comics saw a resurgence with Joe Quesada taking over as editor-in-chief, and the X-Men experienced a renaissance during this decade. However, even as they shone brightly, Marvel was preparing to diminish their role so that the Avengers could once again take center stage.

In the 2000s, some of the most outstanding X-Men tales were produced. Notable comic creators made their mark on X-Men books during this period, resulting in a wealth of top-tier stories for readers to enjoy. Many fans even consider the X-Men stories of the 2000s equal to those from the ’80s. This decade saw some truly exceptional and creative X-Men comics. Here are ten X-Men stories that stand out as the best of the 2000s, leaving a lasting impact on fans for years to come.

10) “Exogenetic”

Warren Ellis’s tenure on Astonishing X-Men has been largely forgotten over time, but it surpasses even the highest expectations. “Exogenetic” encompasses issues #31-35, featuring artwork by Phil Jimenez, and presents the X-Men against an adversary who has meticulously planned his attack for years, employing the most sinister weapons imaginable – the decayed remains of their former teammates. The X-Men encounter a foe who has anticipated them to perfection, one driven by a hatred that, while surprising, is justified. “Exogenetic” is captivating from the very first page, as Ellis delves into some truly bizarre territories. Jimenez’s artwork shines brightest, transforming the script’s grand action sequences into reality and crafting stunning examples of body horror. This X-Men story is unlike any other you’ve encountered before.

9)”Rise and Fall of the Shi’Ar Empire”

In the aftermath of the “House of X” saga, the X-Men’s journey ventured into fascinating realms, and Ed Brubaker’s appointment to the X-Office was a source of great excitement, given his acclaimed work on “Captain America.” Brubaker launched his tenure with “X-Men: Deadly Genesis,” which paved the way for “Rise and Fall of the Shi’Ar Empire,” an extensive twelve-issue storyline illustrated by Billy Tan and Clayton Henry. This saga unfolded in “Uncanny X-Men” issues #475-486, following a team of X-Men, led by Havok, consisting of Polaris, Marvel Girl, Warpath, Nightcrawler, Professor X, and Darwin, as they embarked on a mission to space to prevent Vulcan, the third Summers brother, from annihilating the Shi’Ar in retaliation. This tale is nothing short of epic and remains one of the finest Shi’Ar stories since Claremont’s work. It boasts thrilling action sequences, the reappearance of the Starjammers and Imperial Guard, and a dose of classic X-Men interpersonal drama.

8) “Unstoppable”

Joss Whedon and John Cassaday’s “Astonishing X-Men” is highly appreciated by many fans, but it falls short of its full potential for longtime X-Men readers. It offers a solid tribute to the classic Claremont era of X-Men with impressive artwork and decent character development. While it makes an excellent starting point for newcomers to the X-Men series, those who have been following the X-Men for years might find it not as exceptional as others claim. However, the “Unstoppable” storyline is the pinnacle of the comic book. This final arc concludes all unresolved plotlines by transporting the X-Men to Breakworld for execution, preventing a prophecy that foretells the world’s demise at the hands of an X-Man. The narrative that unfolds demonstrates why the X-Men are the most extraordinary team of heroes. Spanning issues #19 through 24 of “Astonishing X-Men” and issue #1 of “Giant-Size Astonishing X-Men,” it’s an engaging X-Men tale that gets everything right.

7) “Supernovas”

Mike Carey took over writing for volume 2 of X-Men starting from issue #188 and has one of the longest stints among all X-Men writers, surpassed only by Chris Claremont in terms of number of issues penned. Carey delivered some unforgettable Rogue tales and mended the bonds between Xavier, Magneto, and Legion. His run is highly acclaimed and worth reading in its entirety, but if you’re curious about what the buzz is all about, grab “Supernovas”, a story arc that spans from issue #188 to #193 of volume 2 written by Carey, Chris Bachalo, and Clayton Henry. This tale pits Rogue’s quick-action team against the Children of the Vault, a genetically enhanced group designed to annihilate the mutant species. This is the X-Men at their best, a diverse ensemble banding together to confront the gravest danger out there. “Supernovas” truly stands out as a stellar storyline.

6) “Murder at the Mansion”

In this list, Grant Morrison’s “New X-Men” series stands out as the most impressive X-Men run of the 21st century. You can expect more of it here. The initial tale from Morrison’s tenure is titled “Murder at the Mansion”, spanning issues #139-141 of “New X-Men”. Jean Grey uncovers Emma Frost’s psychic liaison, causing tension. When Emma is found in her diamond form broken, the X-Men summon Sage and Bishop from the X-Treme team to identify the culprit. This story delves into Emma’s past while propelling “New X-Men” towards its impending conclusion. Morrison and Jimenez collaborate effectively, having previously worked together on “The Invisibles (Vol. 2)” and in “New X-Men”. This is an engaging X-Men narrative, rich with the soap opera elements characteristic of Marvel’s most complicated team.

5) “Riot at Xavier’s”

In issues #135-138 of ‘New X-Men,’ the storyline titled ‘Riot at Xavier’s’ unfolded, marking Frank Quitely’s final work on the series. Grant Morrison initiated his run with Quitely. The narrative revolves around Quentin Quire, a student at Xavier’s, who learns he was adopted. This revelation pushes him towards rebellion and contempt for humanity. As an Omega-level telepath, Quire gathers a group of like-minded mutants and stages a protest on the school’s latest media day. ‘Riot at Xavier’s’ is one of Morrison’s more intriguing stories, exploring the potential youth culture among mutants. Morrison and Quitely make an exceptional pair, and this story is rich with striking visuals and innovative concepts. It serves as a compelling prelude to ‘Murder at the Mansion,’ showcasing Morrison’s unique take on the X-Men.

4) “Planet X”

Titled “Planet X,” this comic book storyline from the 2000s stirred intense debate among X-Men fans due to its portrayal of Magneto. The narrative revolves around the character Xorn, a peaceful mutant who appears to have a celestial body. However, Morrison skillfully misdirected readers during his tenure with Xorn, as it was later revealed that Xorn was actually Magneto in disguise. This revelation leads Magneto to betray the X-Men and seize control of Manhattan.

Many X-Men enthusiasts were frustrated by this depiction of Magneto as a villain, but “Planet X” is a compelling story that underscores one of Grant Morrison’s key themes in his work – the detrimental impact of hate on the soul. It features an outstanding confrontation between the X-Men and Magneto, culminating in a surprising twist that significantly affected the X-Men for years to come. If you ignore the negative opinions, “Planet X” is undeniably brilliant.

3) “Assault on Weapon Plus”

In an earlier phase of his work, Morrison introduced one of the century’s most captivating mutants, Fantomex. However, due to delays and hasty artwork during Igor Kordey’s tenure, readers didn’t experience a well-illustrated Fantomex tale until “Assault on Weapon Plus” in New X-Men issues #142-145, graced by artist Chris Bachalo. In the storyline “Murder at the Mansion,” Wolverine tracks down Cyclops after his departure from the X-Mansion at the Hellfire Club and enlists him for a mission to the World, the origin of Fantomex and the Weapon Plus program. This journey leads the mutants into one of the most bizarre realms they’ve ever encountered. “Assault on Weapon Plus” is a testament to Morrison’s brilliance, as he showers readers with thought-provoking sci-fi concepts and thrilling action sequences. Bachalo’s artwork complements this tale beautifully, and there are scenes that will leave you speechless. “Assault on Weapon Plus” is an exceptional read – don’t miss out!

2) “Ghost Box”

Warren Ellis’s run on Astonishing X-Men is nothing short of remarkable, with the exceptional quality starting from his initial tale in the book. The storyline “Ghost Box” spanned issues #25-30. Ellis collaborated with artist Simone Bianchi, creating a blend that can be likened to a fusion of Morrison and Whedon’s styles.

In “Ghost Box”, the X-Men stumble upon the remains of an unrecognized mutant, an occurrence that would have been inconsequential in the past. However, with their current global access to all mutants, this discovery raises questions about potential hidden mutants. In pursuit of answers, the team embarks on a journey around the world, uncovering clues that lead them to a spacecraft cemetery, a covert Chinese mutant city, and the madhouse of an ally. All these destinations serve to shed light on the mystery at hand.

“Ghost Box” epitomizes top-tier X-Men sci-fi, with Ellis demonstrating a near-flawless understanding of the team’s voices. Bianchi’s artwork is exceptional; his distinctive and intricate style lends an otherworldly atmosphere to the story, making it truly stand out. This is undoubtedly peak X-Men material, and it’s unfortunate that it isn’t discussed more often.

1) “E Is for Extinction”

In issue #114 of the X-Men comic series, Morrison and artist Frank Quitely made their debut. Their initial story, titled “E Is for Extinction,” spanned issues #114 to #116 and was hailed as the finest X-Men tale of the 2000s. This groundbreaking three-part series significantly altered the X-Men’s standing by transforming them into mutant rescue workers, introducing Cassandra Nova, revealing the mutant boom and the extinction gene in humanity, and welcoming Emma Frost to the team. “E Is for Extinction” encapsulates the best aspects of the X-Men and Grant Morrison, with Quitely’s unique art providing readers with unforgettable visuals. To this day, no X-Men story has managed to feel as innovative as this one, even after more than twenty years.

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2025-07-07 16:14