The X-Men are coming to the MCU in the near future, and while fans wait with great anticipation to see how the mutants will be interpreted, the comics may hold some clues. A lot of the MCU has drawn from more recent comics from the 2000s, and some of the best issues of 2000s era X-Men might provide a blueprint as well.
The 2000s saw some of the biggest creative reimaginings of the franchise in its history, with the Grant Morrison run on New X-Men and the Ultimate Comics reboot occurring around the same time. It also provided some of the biggest events in Marvel Comics history, some of which are likely to find their way into live-action.
Ultimate X-Men #1
Ultimate X-Men #1, written by Mark Millar and drawn by Adam Kubert, is a critical issue in the history of X-Men, as it's the biggest wholesale reimagining of the franchise since Giant-Size X-Men #1 in the 70s.
This story takes place in Earth-1610 and reboots and remixes X-Men history and characters in intriguing ways, introducing characters like Wolverine into the mix from the beginning and taking a darker approach to the story that would be typical of Millar's work both within Marvel and in his own creator-owned comic books like Jupiter's Legacy.
Uncanny X-Men #450
Writer Chris Claremont and artist Alan Davis, who collaborated on the 80s Excalibur run, reunited for issue #450 of Uncanny X-Men, which brought X-23, Laura Kinney, to the team. The issue is great for a number of throwbacks - including the brown and yellow costume X-23 wears, similar to a classic one by Wolverine - but also a reference to the events of Excalibur #16.
As much as this issue looks back, it's key for being a clear demarcation point between the past and the future. With the arrival of X-23, the X-Men would never be the same.
X-Statix #1
X-Statix #1 from 2002 represents one of the most unique and refreshing takes on the world of mutants in this period. The dark and often splashy X-Force comic book issues of the 90s are completely reimagined by writer Peter Milligan and artist Mike Allred into a fun, irreverent story full of strange new characters like Doop.
The first issue features the death of a significant character but is otherwise an oasis of fun and color in what would ultimately become a very dark decade for the world of mutants, making this issue all the more rewarding.
X-Men #188
X-Men #188 from 2006 is a great issue for a number of reasons. One of the most important is the introduction of the Children of the Vault, strange and powerful villains who factor significantly into the current run of X-Men comics and are likely to for some time to come.
Written by Mike Carey and with excellent art by Chris Bachalo, the issue is also a lot of fun, uniting Sabretooth, Mystique, Emma Frost, and others under the leadership of Rogue as she leads them into a dangerous mission.
Uncanny X-Men #468
Rachel Summers is one of the most powerful mutants and key for the prospect of the multiverse, and she is the only version of the character throughout the infinite realities in Marvel Comics. Despite this, she's been an afterthought at times.
Uncanny X-Men #468 is a great issue for providing Rachel a singular identity as Marvel Girl - taking on the surname of Grey to honor her then-late mother, Jean. Rachel begins to come to terms with the dark past she has left behind as a member of one of the best alternate versions of the X-Men in the Days Of Futures Past timeline.
Astonishing X-Men #1
As much as the early 2000s were about reinventing the X-Men, Astonishing X-Men #1 from 2004 is about going back to basics.
After a few years of wearing movie-inspired outfits and deconstructing the concept of the X-Men under Grant Morrison, the team goes back to the comic book colors and more traditional adventures. The outcome is anything but ordinary though, as the character dynamics and extraordinary art by John Cassaday bring together classic X-Men in new situations that see them grow and change.
NYX #3
NYX #3 is the first appearance of Laura Kinney, X-23, and one of the most significant issues of the period. Now codenamed Wolverine and part of the new X-Men team, Laura has had an amazing journey and it all begins here.
The story, written by Marvel editor-in-chief Joe Quesada, is a dark tale indicative of the time. This 2004 limited series wasn't formally part of the Marvel Knights imprint, but with mature themes and evocative art by Joshua Middleton, it's one of the best issues of the time and most important.
House Of M #7
House Of M is a major comic book storyline that inspired WandaVision, and issue #7 of features one of the most important moments in Marvel Comics history. The Scarlet Witch erases all but a handful of mutants from existence, setting off a landslide of consequences that are playing out to this day in the comics.
Most modern X-Men comics are founded on this event, which depicted Wanda lashing out against those who interrupted the false reality she had constructed in which both her children were still alive. Some aspects of the story were realized in WandaVision, but other elements could also be depicted as the MCU goes forward.
New X-Men #114
Grant Morrison created one of the most complex and unique runs in the history of X-Men with his time on New X-Men. Issue #114 completely reinterprets the X-Men by giving them all-new black leather costumes like the Fox movies, introduces the concept of secondary mutations, most importantly for Beast and Emma Frost, and creates a complex new villain in Cassandra Nova, Xavier's twin sister.
The wild ideas and complex threads Morrison has been famous for in their other work are all here, making this issue a key place to start.
Giant-Size Astonishing X-Men #1
The Astonishing X-Men run in the early 2000s ends with Giant-Size Astonishing X-Men #1, and one of the most dramatic uses of Kitty Pryde's mutant powers in Marvel Comics. She uses her ability to phase other solid objects to render a giant space bullet intangible and phase it through the entire Earth.
This leaves her trapped on the bullet and lost in space, setting up events for years to come. It's a major moment for Kitty Pryde and a fantastic issue that brings to a close one of the best runs for the X-Men in the 2000s.