So, you want to start reading X-Men comics again but it's been years and you're feeling overwhelmed at the thought of everything you might have missed. That's understandable—X-Men consists of multiple ongoing series, a constantly expanding cast of characters, and decades of convoluted (and sometimes contradictory) continuity. Don't fret, here's all you need to know to get caught up.
Mutants became an endangered species.
First there was the Sentinel attack that wiped out 16 million mutants by destroying the island of Genosha in New X-Men #115. Then, in the mini-series House of M, Magneto's daughter, Scarlet Witch, decimated the mutant population with a simple three word spell: "No more mutants." This de-powered all but a few hundred of the mutants in the Marvel Universe, but don't worry, most of the A-list mutants were left untouched.
A few years later, in the three-part series of Messiah Complex, Messiah War and Second Coming, the first post-Decimation mutant was born and is aptly named Hope. After being brought to the far future to grow into an adult under the protection of the mutant Cable, a grown-up Hope is returned to present day and she happens to look very much like another red-headed mutant of great importance: Jean Grey.
Jean Grey died. Again.
Jean Grey and her symbiotic relationship with the Phoenix Force is one of the most epic ongoing plot threads in X-Men history. At the end of the "Planet X" storyline in New X-Men #150, Jean once again taps into the powers of the Phoenix only to be killed by an insane Magneto (who may not really have been Magneto, depending on whether you believe writer Grant Morrison's intentions or the subsequent writers who later contradicted him).
Before her death, Jean and her husband Scott (Cyclops) Summers found themselves growing apart. Scott began a telepathic affair with former villain-turned-X-Man Emma Frost, and with Jean gone, Scott and Emma became a couple.
Professor X died, too. Again.
The Phoenix Force returned to earth in the 2012 mini-series Avengers vs. X-Men, threatening all of existence. The assumption was that it was coming back to inhabit the so-called "Mutant Messiah" and Jean Grey look-alike Hope Summers. But everyone was wrong.
Instead, the Phoenix merged with five separate mutants: Cyclops, Emma Frost, Piotr (Colossus) Rasputin, his sister Illyana (Magik) Rasputin, and Namor, the Sub-Mariner. The "Phoenix 5" used their nearly omnipotent power to try to remake the world into a better place until its corruptive nature turned them on each other. In the end, Cyclops takes in the power of the entire Phoenix Force himself and, when confronted by Charles Xavier, lashes out and kills him.
New mutants are popping up everywhere.
Scarlet Witch and Hope Summers manage to wrest the Phoenix from Cyclops and, before casting it away, Hope uses its power to restore the mutant population, reversing the damage the Scarlet Witch had previously done. Now, people all over the world are suddenly manifesting mutant powers and the X-Men are divided in how they aim to help these new mutants.
Cyclops is the most wanted mutant in the world.
Cyclops has always been a bit of a boring character, but over the past 10 years he's gone through some dramatic changes. After killing Professor X, he has become Public Enemy No. 1 and hated by many of his fellow X-Men. He is also the poster boy for a more militant wing of mutantdom. Like a mutant Che Guevara, he sets up headquarters in the old, abandoned Weapon X facility and leads a new team of X-Men with Emma Frost and Magik.
Cyclops' radicalization had been building for a long time and manifested itself originally in a clash of ideals with Wolverine. Cyclops now stands for the idea that mutants need to militarize while Wolverine has taken up Xavier's mantle of peaceful coexistence and the need to protect and educate younger mutants.
Wolverine is the headmaster of the Jean Grey School for Higher Learning.
The idea of Xavier's school being an actual school full of actual students only became the status quo around the time of the first X-Men movie in 2000 and Grant Morrison's New X-Men series around the same time. With Xavier dead and the school destroyed by Magneto, Logan has built a new one called The Jean Grey School of Higher Learning and brought in Kitty Pryde, Iceman, Storm, and the Beast to teach the students.
(Edit: A reader in the comments below pointed out that the Xavier school was actually destroyed by Sentinels which happened during the Messiah Complex storyline).
The original X-Men have time-travelled to the present
(And Jean Grey is back)
The threat of a dark, dystopian future has been at the heart of many X-Men stories since Chris Claremont and John Byrne's classic 1981 "Days of Future Past" (the inspiration for the upcoming new film). In Brian Michael Bendis and Stuart Immonen's new series All New X-Men, they have brilliantly turned this idea on its head by making our present the dystopian future that needs to be avoided at all costs.
In a desperate plan to prevent Scott Summers from becoming the Professor X-killing mutant terrorist he is today, Hank (Beast) McCoy travels back in time to the early days of the X-Men and brings the original teenage versions of himself, Cyclops, Iceman, Angel, and Jean Grey to the future to show them how messed up things have gotten. Even though their very presence endangers the timeline, they decide to stick around, figuring Professor X will just wipe their memories when they go back (or something).
So, not only do we have Jean Grey back, but suddenly there are brand new relationship dynamics to be explored. The original X-Men now look up to Kitty Pryde as a mentor. Jean, Scott and Angel have to deal with the terror their future lives have become (did I mention that Angel died during Uncanny X-Force's "Dark Angel Saga" but came back with amnesia?). Even the love triangles have become more complicated (Do Jean and Scott really love each other? How do older Scott and Logan rectify their feelings for Jean with this teenage girl that's now before them? Does Jean have feelings for Hank? And what does Rachel Grey, Scott and Jean's grown daughter from the future, think of all this?).
There are a LOT of different X-Men books now
At some point in the 1990s, the X-Men became way too big to be contained by just one book. Here is a brief rundown of the major books and what they're ostensibly all about:
All New X-Men: This is a new title that began last year. Its main focus is on the introduction of the original young X-Men into the present day timeline, but it operates pretty close to the center of the X-Men universe and involves a large cast of characters including Wolverine, Kitty, Iceman, and Beast (in addition to the time-displaced young X-Men).
Uncanny X-Men: The original flagship title has gotten smaller in scope since its relaunch. It follows Cyclops and his renegade team of Magik and Emma Frost as they build a new school of students that have just manifested mutant abilities. It crosses over a bit with All New X-Men, especially in the beginning.
X-Men. This is sometimes referred to as "X-Women" since it follows a loose-knit team of female X-Men including Storm, Rogue, Psylocke, and Jubilee, among others. It aims to be a high-octane, non-stop action comic for fans of 1990's era X-Men.
Wolverine & The X-Men: This book focuses on the Jean Grey School of Higher Learning and its cast of students. This is the fun, light-hearted X-Men comic, mixing high school melodrama with ridiculous sci-fi concepts. There is a quirky mix of students, and part of the fun is seeing characters like Logan and Kitty stepping up into their new roles as teachers.
Amazing X-Men: This comic is only a couple of issues in and aims to be the one for fans of 1980s era X-Men. The plot (so far) involves the return of long-dead fan favorite Nightcrawler.
There are also a lot of books featuring related X-teams like Uncanny X-Force, Cable and X-Force, All New X-Factor and Uncanny Avengers (a hybrid team of X-Men and Avengers).
Where you should start
The biggest story being told right now is happening in All New X-Men and it's really the most enjoyable of the books at a time when, overall, the X-Men comics are the most interesting they've been in years. It's written by Brian Michael Bendis with art by Stuart Immonen. Start with #1 or the first collected volume titled "Yesterday's X-Men."
Buy the first volume on Amazon.com or ask your local comic book store retailer. You can also buy the collected volume or individual issues digitally on Comixology.