Professor X has the ability to use his legs back in this issue as a result of the T-O virus Stryfe infected him with. Jubilee takes him rollerblading, Gambit tries to make out with Rogue, and Beast and Archangel rebuild Harry's Hideaway destroyed by Caliban.

Part 2 of The X-Cutioner's Song, the issue came with a Stryfe' Strike File card featuring Caliban.

Doctors try to save Professor X's life as he is rushed to the hospital where Taylor of the X-Patriots is. The doctors learn that he's been infected with a techno-organic virus spreading rapidly and they can't do anything to save him.

Meanwhile, X-Force is upset and on the hunt for Cable who they believe to have made the assassination attempt on Xavier. At the scene of the crime, they instead find Strong Guy and Wolfsbane along with a livid Archangel. Wolfsbane beats up Feral and X-Force retreats when the rest of X-Factor and the X-Men blue team arrives and attacks. Havok damages X-Force's quinjet as they escape.

Apocalypse's Horsemen present an incapacitated Cyclops and Jean Grey to what they believe to be Apocalypse. After the Horsemen leave Mr. Sinister reveals himself.

Part 4 of the X-Cutioner's Song

A knock-out drag-out fight involving almost every character in the X-books. X-Factor and the X-Men hunt down X-Force in hopes of finding Cable who they believe attempted to kill Professor X. An immense battle ensues, half of X-Force is injured and the other half retreats, eventually surrendering.

The Gold X-Men team hunts down Apocalypse's Horsemen and take them down in a warehouse.

Cable is back in the present and readying himself.

Mr. Sinister shows up at the X-Mansion and threatens Val Cooper and Stevie Hunter. Bishop shoots him in the head to no avail, Sinister departs after leaving a message about who the X-Men really need to be worrying about.

Forearm and Reaper present Jean Grey and Cyclops all wrapped up to Stryfe who calls them mother and father.

Part 6 of the X-Cutioner's Song, this issue comes bagged with a Polaris & Havok Stryfe's Strike File card.

In Department K, Bishop and Wolverine attack Cable who they believe tried to kill Xavier. Bishop wants to kill Cable but Wolverine breaks his gun and Cable convinces them to stop fighting and hear him out.

Apocalypse climbs to one of Cable's safe houses in Switzerland and realizes who is really behind the abduction of Cyclops and Jean Grey and the attempt on Xavier's life.

The X-Patriots knock out and abduct one of Madrox's dupes at the hospital Taylor was at.

Meanwhile, the X-Men, X-Force, and X-Factor find Stryfe's Mutant Liberation Front in an underground complex in Arkansas and a battle ensues. Archangel accidentally decapitates Kamikaze while fighting Forearm, the head rolls in front of Boom Boom and makes he sick. Wildside gets the best of Gambit and Reaper cuts Quicksilver's legs and threatens to behead them both with his scythe.

X-Cutioner's Song Part 8

Stryfe finds Apocalypse and stabs him with the knife he used to kill him at another point in time. The Dark Riders bow to him and swear allegiance to Stryfe.

The Professor briefs Bishop and Wolverine on Graymalkin about Stryfe and the MLF, and the events so far since the attempt on Xavier's life. Cable tells them about the Clan Chosen, his time traveling, and the fact that he and Stryfe are mysteriously identical.

Meanwhile X-Force is locked up in the Danger Room. Siryn learns she was in love with one of Madrox's dupes, not the real one and Boom Boom is being tortured with a broken jaw.

Jean Grey and Cyclops escape from the cell Stryfe had them detained in after learning he was dampening their powers.

Beast is trying to find a way to eliminate the T-O virus from Xavier when a beat up Apocalypse shows up at the X-Mansion offering his services.

Part 10 of the X-Cutioner's Song, this issue came bagged with a Dark Riders Stryfe's Strike File card.

Cyclops and Jean Grey have escaped Stryfe's base and realize they're on the moon and can't breath. Stryfe saves them and suggests that he is their son before torturing them some more.

Wolverine, having received a psionic distress signal from Jean Grey, tells the X-Men and X-Factor that she and Cyclops are on the moon. Cable, Bishop, and Wolverine prep themselves to go to the moon on their own. Upon arrival at the base they run into the Dark Riders and some of Stryfe's MLF troops.

Havok assembles a team of X-Men, Polaris, and Cannonball to go to the moon as well. Madrox lets Havok know the dupe that was watching the X-Patriots was missing. The dupe later awakens in the hospital.

Archangel lets Apocalypse out of the cell he was being detained in to try and save Xavier who was near death. Apocalypse complies and uses a device to eradicate the T-O virus from Xavier's system but not before enveloping Xavier and himself in the virus. Storm and Havok try to stop Apocalypse but Archangel stands in their way seemingly possessed again. Apocalypse and Xavier disappear then reappear as the X-Men look on in horror with the remaining T-O virus on the floor. Storm thanks Apocalypse and he offers use of his spaceship to fly to the moon.

Part 12 of the X-Cutioner's Song, the climax, the big showdown between Cable and Stryfe. This issue came bagged with a Stryfe's Strike File card.

Stryfe and Cable battle on the moon with Cyclops and Jean Grey looking on powerless in an energy field that only those with the Summers gene can penetrate. Stryfe asserts that he is superior to Cable, that Cable was a clone and a mistake.

Psylocke psionically detects that Apocalypse is dying. Archangel finds him near death, defeated by his own Dark Riders. Apocalypse expects Archangel to kill him, but Archangel refuses and leaves him to die.

Meanwhile Havok, having entered Stryfe's energy field awakes after being knocked out by it. He attacks Stryfe who loses his concentration allowing Cyclops and Jean Grey to escape his hold on them. The Summers family pleads with Stryfe to let them help him but he can't trust them and believes they will betray him again.

Cable gives Cyclops a device that activates a time vortex, Cyclops activates it while Stryfe and Cable battle. Both are sucked into the vortex, to what is believed by Cyclops to be their deaths.

The epilogue features Mr. Sinister's assistant Gordon unwittingly opening the cannister that contains the Legacy Virus believing it to contain the Summers DNA.