E Is for Extinction

"E is for Extinction" was the first story arc from Grant Morrison's run on the Marvel Comics title "New X-Men". The story was published in "New X-Men" #114–116 in 2001 (formerly titled "X-Men", the series was renamed "New X-Men" at the request of Grant Morrison, but retained its original numbering). The storyline began Grant Morrison's revamp of the X-Men franchise, introducing a new status quo for the X-Men and the mutant community of the Marvel Universe as a whole.
Plot.
As a new generation of mutants begins maturing across the globe, a long-lost Master Mold A.I. and Sentinel production facility in the jungles of Ecuador is uncovered by a mysterious woman called Cassandra Nova. She uses the last surviving relative of Bolivar Trask to gain control of the wild sentinels and has the man order the Sentinels to massacre the entire population of the mutant nation of Genosha. However, Cassandra Nova's presence shows up on the newly created mutant detection machine Cerebra, created by Beast, leading to Cyclops and Wolverine finding Cassandra and defeating her. But it's too late, as the nation of Genosha falls to the deadly might of the Sentinels and nearly the entire population of the island state is killed off. 
As the X-Men search the rubble, they find former X-Men villain and teacher Emma Frost as one of the survivors, having survived the Sentinel onslaught thanks to her body undergoing a new secondary mutation. At the X-Mansion, Beast investigates the biological origins of the powerful enemy they have just captured, while also revealing the possibility of mankind's genetic extinction within the next few generations. When Cassandra suddenly overcomes her imprisonment and effortlessly makes her way to Cerebra (in order to take over Charles Xavier's mind), Emma Frost (who moments before the battle began had left the X-Mansion, intent on revenge against humans for the genocidal Sentinel attack on Genosha) shows up again to snap Cassandra's neck. But Emma arrives too late, as Cassandra has swapped bodies with Xavier and shoots him (now in Cassandra's body) to keep Xavier from revealing what has just happened. 
Days pass; Jean Grey and Cyclops reflect upon the marital problems that have popped up due to Cyclops's post-traumatic stress disorder (brought on by Apocalypse possessing Cyclops's body for over a year) when they turn on the TV and see "Xavier" out himself as a mutant on live television.
Reception.
Grant Morrison's arrival on the X-Men franchise as the new writer of "" was highly anticipated and featured amongst other things, massive changes for the X-Men franchise. Among which were new designs for the X-Men, where the group abandoned their traditional spandex costumes for leather jackets and conservative turtle-neck sweaters. Additionally, Wolverine and Beast underwent massive visual changes as well, Beast becoming more beast-like than man and Wolverine abandoning his old costume for a new casual look. While the former was and remains controversial with fans (being one of the few elements of the Morrison run not to be reversed upon his departure from the book), Wolverine's new civilian garb (designed to cash in on the success of the X-Men live action film) was warmly received by fans. 
This story also led to the introduction of Cassandra Nova (Professor Xavier's previously unseen twin sister, who escaped from the womb via miscarriage after the two siblings engaged in psychic combat against each other). Nova would ultimately be named "Villain of the Year" by Wizard Magazine for the year 2001, for the genocide inflicted against the people of Genosha.
Secondary mutation.
One of the major aspects introduced in the storyline was the official canonization of the concept of "secondary mutations". The term refers to mutants who possess multiple powers, a longstanding tradition of the X-Men books that had never been officially addressed by writers. The concept was mainly incorporated by Morrison to provide Emma Frost new diamond skin powers, allowing her to serve as a replacement for the recently deceased Colossus.
Collected editions.
A trade paperback of the storyline was released in 2001; the initial printing of the trade paperback included "New X-Men" #117 (which served as a bridge issue between "E is for Extinction" and the next multi-part storyline "Germ Free Generation") and the "Morrison Manifesto", a detailed account of Grant Morrison's proposal for their plans as writer for the X-Men. 
The initial paperback did not have "New X-Men Annual 2001", which was omitted due to issues involving how to reprint the story, which was published in the sideways "Widescreen" format. As the issue contained the set-up for a key number of future major plotlines for the Morrison X-Men run, later printings of the trade paperback removed the "Morrison Manifesto" and replaced it with the annual, which was published in the standard comic format, though still sideways.
The storyline has also been included in other volumes collecting wider storylines:
Secret Wars (2015).
The "Secret Wars" storyline features a new "E is for Extinction" miniseries that is part of the event. Its domain on Battleworld is Mutopia.
Revisiting the first story arc from Grant Morrison's run on the Marvel Comics title , Professor X is holding a gun to his head, ready to shoot himself in order to prevent the twin sister he killed in the womb from make her way to Cerebra (in order to take over his mind). Unlike in the main continuity, where Xavier’s bluff is successful, Xavier is forced to actually kill himself in this timeline. The psychic backlash of his death knocked out Jean Grey and put her in a coma while encasing her inside the Phoenix Egg. 10 years after the death of Professor X, Magneto has his own institute with 90% mutant students, as well as his own team of X-Men consisting of the students who attended Xorn’s Special Class in the original run. A group calling themselves The Patient show up to commit violence on the mutants. They’re presumably humans who have genetically given themselves powers and they want to kill off the real mutants. Magneto shows up with his X-Men, all young and with a few familiar faces like Angel Salvadore, Basilisk, Beak, Dust, Glob Herman, Ernst, No-Girl, Redneck, the Stepford Cuckoos, and Tattoo. Another group of middle-age X-Men eventually do show up, albeit late and pathetic. Cyclops pretends like he’s still the guy leading an entire race, but he just makes a fool of himself. Magneto establishes here that Cyclops and Emma Frost are basically a bunch of has-beens since their powers are fading away. Even the rest of Magneto’s team goes out of their way to berate them and not in a very good way. Meanwhile, at a mutant medical center, Beast is helping out a couple of prospective parents. Apparently, they want to make sure their child is a mutant. In a domain where mutants are the majority, just being normal is basically a handicap so they want to make sure their kid has that advantage. Later, Wolverine is approached by Cyclops at a bar saying he has a mission and it involves Jean Grey. As it turns out Magneto has had Jean Grey locked away at the school for quite some time now. Magneto then explains to Esme Cuckoo that Jean Grey fell into a coma after Professor X killed himself. Apparently, their minds were linked during the struggle against Cassandra Nova. Now she’s stuck in this pseudo-Phoenix Egg and he wants to wake her up. Unbeknownst to him, Cyclops had an informant inside his ranks and discovered Jean was in his possession. To try and save Jean, Cyclops assembled the old X-Men Emma Frost and Wolverine and released Xorn from his prison that was run by the U-Men so that he could help them.
Cyclops' X-Men invaded the Atom Institute and engaged in fight against the new X-Men while Quentin Quire (who was Cyclops' informant) confronted Magneto in the basement. Angry, Magneto used his powers to create a tendril of metal and stabbed Quentin with it, but Quentin had already bonded himself with the egg and started to hatch it. Xorn then emerged in order to destroy it and was attacked by Magneto in response. With his helmet destroyed revealing the miniature star in his head, Xorn battled Magneto ravaging the entire Institute, but vanished when he realized that Jean Grey was not alone inside the egg. Afterwards, the Phoenix Egg went dormant and fell on Magneto seemingly killing him. On account of what happened, Beast was there investigating an unknown viral strain (which killed a human version of himself he found on his doorstep) that was being drawn to the Atom Institute. He said that there were no great power to be derived from the Phoenix Egg and that Magneto was wrong after all. Just then, an army of alternate versions of Beast appeared with one of them saying that Magneto was right.
The old and new generations of X-Men as well as the Atom Institute students, united forces in order to prevent the Beast army from getting the Phoenix Egg which started to hatch once more while they battled. Emma Forst, who had combined her powers with the Stepford Cuckoos to become the Six-In-One, started to shut the Beasts down one by one before turning her attention to their leader. Reading his mind, Frost discovered that the real threat was Sublime, a sentient bacterial life-form which laid hidden inside the Phoenix Egg until it was discovered and used by Magneto. Tired of being used, Sublime managed to spread his spores all over Battleworld, infecting and assembling all the versions of Beasts (its perfect host) it could find to take control of the Phoenix Force inside the egg. Shortly thereafter, Sublime took control over this domain Hank McCoy and used him to kill Esme, breaking the link between the Six-In-One. Sublime afterwards got the upper hand over the X-Men. As everything seemed lost, the disembodied mind of Professor X possessed Quentin Quire's corpse reanimating it and used his powers to finally destroy Sublime ending his threat once and for all. But the battle wasn't over yet as Cassandra Nova emerged from the Phoenix Egg in possession of Jean Grey's body and the Phoenix Force.