The X-Men are one of Marvel's most storied franchises. They've also had some huge ups and downs over the years as well – the book was cancelled until Giant Size X-Men #1 revitalized interest in the mutants, they rode high for years and then got left behind when Marvel decided that to push other comic properties over them. With the recent Dawn Of X initiative, mutants are riding high again... although they may also be sowing the seeds of their destruction in their new books.
There have been a variety of X-teams over the years and more stories than one can shake a stick at. While there are big stories that everyone knows about, there's also a lot of really good stories that have fallen through the cracks.
10 Uncanny X-Men #281
Uncanny X-Men #281 had the unfortunate place of coming out alongside X-Men #1, aka the best-selling comic of all time. However, it's a great comic that more people should read, showcasing Sentinels attacking the Reavers, the X-Men being called to the Hellfire Club, and then the Sentinels attacking everyone in a giant battle that ends with a huge shock.
Written by John Byrne, Jim Lee, and Whilce Portacio with art by Portacio, this is a great single issue that also debuted the Gold Team, one of the most important X-Men line-ups of the '90s. This was just an infinitely re-readable book that doesn't get as much credit for how good it is.
9 X-Men #30
In theory, it's hard to call the wedding of Cyclops and Jean Grey a forgotten story – as the premiere couple of the X-Men, their wedding is an important foundation of the X-Men mythos. However, it's a good bet that not many modern readers have actually read the comic and that's a tragedy. Comic weddings are prone to shenanigans of the supervillain kind and this one has none of that.
It's genuinely a heartwarming comic about the marriage of one of Marvel's biggest couples. Writer Fabian Nicieza and artist Andy Kubert gave readers the wedding these two characters deserved and it's still a great read all these years later.
8 Uncanny X-Men #350
Gambit's whole shtick throughout the '90s was that he was the mysterious one, the guy with all the secrets. Over the years, there were hints that he had worked with Mister Sinister... hints that would be proven by this issue of Uncanny X-Men. In it, Gambit is put on trial by Erik The Red for his role in the Mutant Massacre.
This issue reveals that he led the Marauders into the tunnels and while he didn't kill anyone, what he did was bad enough in the eyes of his fellows. Writer Steve Seagle and artists Joe Madureira and Andy Smith did a great job of paying off years of build-up and it ends with the return of a fan favorite villain.
7 X-Men: Prime #1 (1995)
X-Men: Prime served as a way to reintroduce the X-Men after the seminal Age Of Apocalypse, one of the most beloved X-Men stories of the '90s. Written by Fabian Nicieza and Scott Lobdell and art by Bryan Hitch, Jeff Matsuda, Gary Frank, Terry Dodson, Mike McKone, Paul Pelletier, and Ben Herrera, this set up story lines for all of the '90s X-books.
While it might seem like a waste to read it as it's just a teaser book, there's a lot of quality storytelling and art in this comic along with a central arc about a young mutant trying to get to the X-Mansion as bigots chase them down. It's a lot better than most people realize and a definite gem.
6 "The Twelve"
"The Twelve" served as one of the last X-Men stories of the 90s, wrapping up one of the biggest mysteries of the decade. Apocalypse's plan to take over the world comes to fruition, as he searches for the Twelve – a group of mutants whose powers combined can give him godlike power. Writer/artist Alan Davis spent most of his run building up to this story and it was a pretty satisfying tie-up to the whole plot line of the Twelve.
Playing out through Uncanny X-Men, X-Men, X-Man, Cable, and Wolverine, this is one of those stories that gets overlooked but is filled with great art, writing, and action.
5 Astonishing X-Men #1-3 (1999)
This book is one of the preludes to "The Twelve" and sees Cyclops, Jean Grey, Cable, X-Man, Wolverine, and Archangel investigating an attack on S.H.I.E.L.D. by Death, the Horseman of Apocalypse. Written By Howard Mackie with art by Brandon Peterson, this ends on a huge surprise that plays into what Alan Davis was doing over in the main X-Men books.
While it does play a part in the books of the time, it's also just a good X-Men story with a cool twist ending that will readers to other good stories.
4 Uncanny X-Men #375
This book contains the continuation of the plot lines from Astonishing X-Men – Professor X and the members of the team from AXM call the rest of the X-Men back to the mansion for an autopsy of one of their own... which turns into a massive brawl between the members of the team.
Written by Alan Davis with art by Adam Kubert, this is an action packed issue that pits two sides of X-Men against each other in a no holds barred battle and ends on a surprise twist that will leave readers begging for more.
3 "Magneto War"
Written by Alan Davis and Fabian Nicieza with art by Davis, Lee Weeks, and Leinil Yu, this story partly served as a way to tie up the Joseph story line – an amnesiac Magneto who had been hanging out with the team – and also the triumphant return of Magneto as the team faces down his newest plan to attack humanity... as well as a revenge scheme by a forgotten member of the Brotherhood of Evil Mutants.
Magneto had been out of circulation for a while when this came out and fans were more than ready for his return. It tied up some loose plots from the past and saw Magneto win what could have been his greatest victory
2 "Operation: Zero Tolerance"
"Operation: Zero Tolerance" ran through just about every major X-Men title of the mid-90s and saw Bastion, a mysterious government agent, get permission to enact a plan to take down the X-Men using the Prime Sentinels, humans infected by nanotechnology. Iceman, away from the Mansion at the time of the attack, is forced to bring together a team of disparate mutants to fight back.
One of the best X-stories of the mid-90s, "Operation: Zero Tolerance" is criminally underrated. It comes from a time in X-Men history that most people don't know very much about – the end of the Nicieza/Lobdell years and the beginning of the Steve Seagle and Joe Kelly run – a run that doesn't get nearly enough credit for just how good it is.
1 "Hunt For Xavier"
"Hunt For Xavier" takes place during the Seagle/Kelly run – the X-Men recently battled an ersatz team of X-Men led by Xavier and set out to find the truth – if their leader has completely disavowed them and is trying to replace them. They get more than they bargained for as their leads land them in battle against the Brotherhood of Evil Mutants and a mysterious robot with deeper ties to the team than anyone can imagine.
Tying into both the aftermaths of the Onslaught story and "Operation: Zero Tolerance", this story is an action packed banger that keeps twisting and turning on readers. Seagle and Kelly were at the top of their game here and the art by Chris Bachalo, Adam Kubert, and Leinil Yu in this this six parter from Uncanny X-Men #362-364 and X-Men #82-84.