Mutant pop-star
Lila Cheney organizes a free concert in
Central Park to promote diversity in society and invites
Professor Charles Xavier to speak at the concert. His speech is interrupted by
Stryfe who, disguised as his doppelganger and nemesis
Cable, shoots Xavier with a bullet that infects the professor with a lethal strain of the
Techno-organic virus.
Meanwhile,
War and
Famine, the
Horsemen of Apocalypse, attack
Iceman and
Colossus, distracting them from
Caliban,
who kidnaps Cyclops and Jean Grey.
The Horsemen are working for
Mr. Sinister, who is impersonating the Horsemen's former master Apocalypse. :youngsabo: Mr. Sinister organized the kidnapping as part of his newly formed alliance with Stryfe.
Stryfe trades Mr. Sinister a canister containing the past and future Summers family DNA history, and receives Jean Grey and Cyclops in the exchange. 
While Xavier is rushed to the hospital, X-Factor and the Blue X-Men strike team go after
X-Force, Cable's team of mutants. X-Force, however, is in the dark about Cable's current location (having been separated from him during a
S.H.I.E.L.D.-organized raid of their headquarters). But mutual distrust causes the two groups to attack and ultimately capture X-Force.
Meanwhile, Mr. Sinister doublecrosses Stryfe by revealing to the X-Men that Stryfe, under the guise of Cable, was the shooter. 
While the Blue X-Men strike team, X-Factor,
Boom Boom and
Cannonball go after the
Mutant Liberation Front,
Storm's Gold X-Men strike team, along with
Quicksilver, confront Apocalypse over Scott and Jean's kidnapping, hoping as well to gain a cure for the virus that is threatening Xavier's life.
Apocalypse is incredibly weak,
having been nearly killed by Cyclops in their previous encounter and prematurely awoken from his regeneration chamber by his minions the
Dark Riders. After learning from the Dark Riders that someone had been impersonating him, and ordered his old minions to kidnap Jean and Scott,
Apocalypse barely escapes with his life.
Archangel finds himself becoming more and more consumed with punishing Apocalypse for his crimes, most notably Apocalypse's converting Archangel into the blue-skinned, metal winged angel of death.
The Mutant Liberation Front is defeated,
though at the cost of
Rogue being blinded by MLF member
Strobe. Meanwhile
Bishop and Wolverine locate Cable and after a brawl, decide to give him the benefit of the doubt and work together to find Jean and Scott.
[that trio
]
Apocalypse is ambushed by
Stryfe,
who declares that he is out for revenge for unknown wrongs committed against him as a child by Apocalypse.
After Stryfe stabs him in the chest, Apocalypse escapes and seeks refuge amongst the X-Men,
ultimately curing Xavier of the
techno-organic virus as payment for
sanctuary.
Cyclops and Jean are systematically tortured by Stryfe :demonic
:, who blames the two mutants for ruining his life, a claim that leaves the two X-Men stunned since they never encountered Stryfe before their kidnapping.
Stryfe and his new minions the Dark Riders, who pledge their allegiance to Stryfe after he defeats Apocalypse, move the two to Apocalypse's former base on the Moon. Scott and Jean escape, entering the vacuum before realizing they are not on Earth. Her powers no longer blocked, Jean sends a frantic SOS to Wolverine
The X-Men, knowing Xavier will live now that Apocalypse has purged the techno-virus from him, head into space to save their teammates. Cable, Wolverine, and Bishop head out to Stryfe's base on the Moon too and arrive there first, decimating Stryfe's defenses just as the X-Men (
Storm,
Psylocke,
Polaris, Cannonball,
Havok, Iceman and Archangel) and Apocalypse arrive.
Splitting up, Apocalypse is ambushed by the
Dark Riders, who beat their former master to the brink of death
.
Apocalypse is later confronted by Archangel who refuses Apocalypse's request for a mercy killing 
.
Upon catching Jean and Scott Summers outside the moonbase, Stryfe takes them to a giant time portal he had constructed on the Moon.
As Cable, Cannonball, Havok and Polaris make their way to the tower, a forcefield is activated that prevents any without the Summers DNA from approaching the tower 
just as Stryfe activated the tower's time portal technology.
Stryfe planned this so he could confront Cable alone, and though Havok has enough genetic similarity to Scott to pass through the forcefield, doing so renders him unconscious. Cable finds himself hopelessly outmatched by Stryfe, but as they battle, Jean Grey and Cyclops break free and Havok regains consciousness. Driven to despair, Stryfe tries to collapse the active tower upon the X-Men. Cable grabs Stryfe and orders Cyclops to activate the time vortex, a plan that would kill both Stryfe and Cable. Cyclops reluctantly does so; both men are sucked into a massive vortex that is created as the tower explodes
. Cyclops and Jean Grey begin to suspect that either Stryfe or Cable is Cyclops' son Nathan Christopher Summers, who Cyclops was forced to abandon and send into the future after Apocalypse infected him with a techno-virus. 
Mr. Sinister has a minion, Gordan, open the canister given to him by Stryfe, only to find it apparently empty
. Though not revealed in
X-Cutioner's Song, the canister in fact contained the
Legacy Virus.
Epilogue[edit]
Professor X discovers that the techno-organic virus has left him temporarily capable of walking and spends his few hours without paralysis bonding with
Jubilee.
Rogue and
Gambit hang out together as Rogue agrees to let Gambit be her "eyes" until she regains her sight, laying the groundwork for the two finally becoming a couple.
Archangel and
Beast rebuild the bar that Cyclops and Jean Grey were kidnapped in and think back to their days as the original X-Men.
Fanboys hate on Stryfe these days but he should of ended up being Scott's real son so that the effects would. Never go away. Thought his armor was dope too.
