X-Men: The End Book 3: Men and X-Men
The X-Men (including Professor X and Magneto, in person) take the battle to the Shi'ar. It is revealed that Khan is Lord Chancellor of the Shi'Ar empire, i.e., the administrator of law, with Lilandra being just the figurehead after being driven insane by Cassandra Nova. It was his plan to destroy the X-Men and kill Lilandra to get the Shi'ar throne. Gambit, however, instantly recognizes Khan - they battle and end up killing each other.
As the X-Men (Cyclops, X-23, M, Captain Britain, and a few others arriving through the wormhole created by Magneto and his daughter, Lorna) begin to battle Lilandra's guard on Chandilar (the Imperial Shi'ar throneworld), the Starjammer arrives in orbit. Storm, Iceman, and a few others form a Plan B contingent and fly to Chandilar in an X-Jet via a space portal.
It is revealed that Cassandra Nova is the mastermind behind everything. She has been hiding in Xavi, the son of Lilandra and Xavier, all this time. She begins to reveal herself to everyone involved, starting with Xavier (who, thinking she was inhabiting Lilandra, mistakenly kills her). On the Starjammer, the Brood eggs have multiplied thanks to Aliyah and have begun landing on the Shi'ar's home planet. Also, Cassandra reveals herself to the Phoenix through Aliyah's mind. The Brood, having made a deal with Cassandra, begin attacking X-Men.
Cassandra Nova attacks the X-Men and the Shi'ar Imperial Guard. She then begins to erase Xavier's mind. Marvel Girl summons her residual Phoenix Force energies and engages Cassandra in psychic battle. Meanwhile Cable uses his vast telekinetic powers to fight Cassandra on the physical level, but succumbs to his techno-organic virus he was infected with as a baby and re-infected with in book one.
Jean Grey, once again the Phoenix, uses her powers to heal Cable, when, suddenly, she (and Cyclops) are killed by a psionic blast fired by a mind-controlled Marvel Girl. Cassandra's astral form leaps out of Marvel Girl's mind, and merges with the Phoenix Force. Cassandra begins killing the Imperial Guard, and Dazzler fires a laser beam through Cassandra's forehead, burning a hole in it, while Storm and Iceman hit her with their elemental powers. However, Cassandra rises from defeat and, in a form of divine punishment, blows a hole through Dazzler and turns Iceman's and Storm's powers against them, killing Storm as well. Only Madelyne Pryor, who has been impersonating Dust (thanks to her black niqāb) all along, after killing her in Book 1, stands in her way. Madelyne reveals that she is the part of Jean Grey that loved Scott with all her heart, and that was the reason that Cyclops' and Jean's marriage failed. Madelyne turns into energy and fuses with Jean Grey, who awakens and heals Cyclops.
As Jean Grey (still able to access some of her Phoenix powers) and Nova fight, Psylocke enters the fray and plunges her psi-katana in Cassandra's brain, immobilizing her. Jean Grey tells Cassandra that they are all going to transcend reality. Jean resurrects all of the defeated/dead X-Men, bringing some with her to become one with the universe while bringing others back to Earth. Xavier and Cassandra admit that they are scared of each other, and Jean tells them that this is part of being human. Then, she and the resurrected X-Men form a giant Phoenix and become part of the universe itself.
The remaining X-Men not part of the Phoenix are seen 20 years later, when Katherine Pryde becomes President of the United States. She disbands the X-Men, saying that the X-Men were their own worst enemy, and that it was time for something new. She emphasizes this is not an end, but a beginning.
In the final frames, as Kitty Pryde makes a speech, Wolverine is shown together with Psylocke, and X-23 behind him. Emma Frost is shown with her grown up children. Mystique is shown with her two grandchildren, Gambit's son is holding a baby. Beast is shown with Cecilia Reyes and their three children. Iceman and Magma are shown together. Sam Guthrie (Cannonball) is shown with his wife, Lila Cheney, and their trio of children. Kurt Wagner, Nightcrawler, is shown with his wife and two children. Aliya Bishop, now the Majestrix of the Shi'Ar is shown with her father, Lucas Bishop, now an Imperial Chancellor. Jean Grey (Phoenix), Marvel Girl, Gambit and Rogue, Havok and Lorna, Alpha Flight, Professor X and Cassandra, Storm, Archangel with Husk, Cyclops, Madelyne, Dust, Cable, Lilandra, Sage, Colossus, Hub, and a few others are shown above the crowd looking down from the other side, as it were.
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