X-Men Chronicles # 1 - Origins

At the top of Wundagore mountain located somewhere in Eastern Europe, Magneto looks down on the X-Men training facility. It is then revealed that the story is set in an alternate reality in which Professor X had died, changing the course of time and making Magneto the head of the X-Men. Soon after, Pietro approaches Magneto to inform him that the X-Men are waiting for him to arrive in order to begin their training exercise at the facility.

When Magneto arrives, several of the X-Men, including Jean-Grey, Collasus, Scarlett Witch, and Storm are successfully sparring against battle androids as part of their training. After disposing of the androids with ease, the team begins to celebrate, only to be interrupted by Magneto who tells them that they are performing below his expectations. He then increases the difficulty of the exercise and the X-Men begin to panic under the pressure. As they find themselves struggling to keep up with the training, Magneto opens a door and a mysterious figure leaps forward, and within moments destroys all of the battle androids. The mysterious figure is revealed to be Weapon X.

After destroying the androids, Weapon X goes into a berserker rage and attempts to harm the other X-Men until Jean goes into his mind and brings him back to sanity. As a result however she becomes overwhelmed by his memories. Pietro grabs her before she falls unconscious to the ground.

In New York City, Apocalypse's ship begins to fly over the city. A holographic image of Candra is then projected throughout the city as she announces Apocalypse's plan for world domination to the public.

Back at the X-Men facility, Magneto is in his quarters pondering on the death of Charles Xavier when he is approached by Mystique who brings him information of Apocalypse's plan as well as a new student, Rogue. After saying her goodbyes to Rogue, Mystique becomes saddened from the farewell and leaves crying. Ice-man, Wolverine, and Jean then enter the room to meet the new addition to the team. Rogue seems reluctant to introduce herself. Fearing that anyone touching her would have their power drained, she throws Ice-man aside the moment he touches her when introducing himself. Magneto then calms her down letting her know she is safe with the X-Men. Jean begins to help Rogue adjust to living with the X-Men by giving her a tour of the facility. As they approach a statue of Charles Xavier, Magneto appears and reminisces on his friendship with Xavier before his death. He is soon interrupted as Pietro runs over to tell him that Apocalypse's horsemen are attacking the Cape Citadel military base.

At Cape Citadel, Apocalypse's horsemen consisting of War, Death, Chandra, Gideon, and Sabretooth begin attacking the base. The military begins to fight back but to no avail, they are eventually defeated. As the horsemen take command of the bases computers, they begin initiating the launch of all nuclear weapons in the United States. Sabretooth however realizes the repercussions of what would happen if they went through with it and orders them to stop. Soon after, Apocalypse is heard over an intercom condemning Sabretooth and orders the rest of the horsemen to kill him. Before they do however, they are interrupted by the X-Men's arrival. Chandra lets Sabretooth go claiming he will either die in battle or be killed by them later.

The X-Men and the horsemen begin to fight one another with the X-Men becoming victorious. Magneto stops the launch initiation by destroying all the electronics within the base using an electro-magnetic pulse. As a result, the base explodes with Magneto inside. Apocalypse then flies over the now destroyed base praising Magneto's death and calling his horsemen to return to ship. He proceeds to launch his ships missiles to the kill the X-Men, but before they strike, Magneto comes out of the rubble and creates a magnetic barrier protecting them. Apocalypse departs, abandoning the heavily wounded Sabretooth because he deems him unfit to be a horsemen any longer.

When the X-Men return home, they find that their facility had been attacked. While they had been fighting the horsemen, Apocalypse's aid, Nemesis had launched a secret attack on the X-Men's defenseless facility. Upon the X-jet's landing, Magneto finds his daughter Scarlett Witch dying and holds her as she passes away.