Chapter XI : The Twelve
As was their lot in life, the X-Men continued to have struggles from both within as well as without. During one such tumultuous period, Professor Xavier had disbanded his X-Men, claiming that the dream he had was misguided. Shortly thereafter, a call for help was heard from some of their allies, and a hastily formed team of X-Men was assembled. During the course of that mission, the X-Men faced an armored, sword-wielding foe, calling himself simply Death. Taking on the whole team, only after massacring all personnel in a secured government facility, Death managed to escape. Before disappearing, Death did the unthinkable and killed Wolverine. [Astonishing X-Men (2nd series) #3]
After the team returned to the mansion, the X-Men made a startling discovery, the Wolverine whom Death had slain was not their old teammate, but a shape-changing Skrull. With this revealed, Xavier admitted that the disbanding of the team was a ruse. For some time, he had been convinced that the team had been infiltrated and created the deception to expose the culprit. With the Skrull revealed, he could now admit the truth. But the question remained, where was the real Wolverine ?
The course of the investigation led the team to Egypt, where they discovered a secret Skrull base of operations. Operating on behalf of their “Ally” to assist in the location of the Twelve. Making short work of the stationed Skrull troops, the X-Men were surprised by the appearance of Death. During the battle, the mask of Death was removed, revealing his true identity. [Uncanny X-Men (1st series) #375, X-Men (2nd series) #95, Wolverine (2nd series) #145]
Wolverine/Death escaped, but the X-Men now knew their true adversary, Apocalypse. Evidently, Apocalypse had been gathering new Horsemen for a new scheme. As the Twelve were mentioned by the Skrulls and the situation with Wolverine seemed to coincide with recently discovered texts in the late precog Destiny’s diary, the X-Men knew that a dark struggle was ahead. Before the X-Men could discern a course of action, various mutants, all listed in Destiny’s prophecies, were abducted by Apocalypse’s new Horsemen. Wishing to take the battle to Apocalypse, the assembled X-Men return to Egypt for the final confrontation. Once the X-Men arrived, the Skrull allies of Apocalypse manage to kidnap the remainder of the Twelve, teleporting them deep inside the pyramid fortress of Apocalypse.
Having assembled his selected subjects, Apocalypse inserted them into a gigantic device of Celestial design. Inside the “null orbs” were Xavier, Cyclops, Phoenix, Storm, Iceman, Sunfire, Polaris, Cable, Bishop, the newly found Mikhail Rasputin, the Living Monolith and Magneto. On the verge of his ultimate triumph, Apocalypse could not resist the urge to gloat at scope of his success. Citing the cryptic prophecy known as the Twelve, Apocalypse claimed that he initiated the prediction in order to gather the precise mutants to power his Celestial machine. Lacking the original energy source that would be require to power the machine, mutants with the correct type of abilities were needed instead. The machine would funnel all of the mutant energies through the Living Monolith so that Apocalypse could absorb them. To ensure that he could contain these great energies, Apocalypse would take the body of Nate Grey, currently the most potent force on the planet, as his own.
Activating the machine, Apocalypse began to bathe in the energies it produced. On the cusp of victory Apocalypse roared in anger as he realized that the 
machine was now malfunctioning. Unbeknownst to Apocalypse, Magneto had recently lost his powers, leaving his part in the Celestial machine unfulfilled. Deciding to make do with only eleven, Apocalypse continued his merger with Nate Grey. The failure of the machine to function properly, however, allowed the captive X-Men to escape their null orbs and press the attack. Trying her best to stop the mad mutant, Phoenix attempted to telekinetically tear Apocalypse apart. She succeeded, but in a manner that took her and the X-Men completely by surprise.
Shrugging off the attack from Phoenix, Apocalypse continued his merger with Nate Grey. Very aware of the powerful psionic abilities possessed by Nate, Cyclops knew that the merger between he and Apocalypse would spell doom for the X-Men and the entire world. Seeing no alternative, Cyclops lunged at Nate, pushing him out of the energy vortex containing he and Apocalypse. Now trapped in the energy vortex in Nate’s place, Cyclops fulfilled the merger process with Apocalypse, and from their union a new being was formed.
Although successfully merged, Apocalypse’s ultimate plan, that of the Celestial machine endowing him with ultimate power, was unfulfilled. Attempting to complete the transformation, he used some of his new powers to warp reality for his previously captive Twelve. Warping reality into various scenarios, Apocalypse hoped to prompt the Twelve into using their powers and, unknowingly, charge the Celestial machine. These differing realities would be known as the Ages of Apocalypse. Several of these scenarios almost succeed, but eventually the mutants realized their true predicament and awakened to the real world. Realizing that his ultimate goal would not be successful, “Cyclopalypse” teleported away from the angry X-Men. The villain having escaped, the X-Men and Phoenix were faced with the horrific fact that Cyclops existed no more. [Twelve crossover]
Chapter XII : Return to Akkaba
In the months that followed, the X-Men attempted to recover from the blow of Cyclops’ apparent death, and begin anew. As a symbol of this new beginning and dedication, Cable, Cyclops’ son, joined the X-Men. Despite his vast disagreement with the vision of Xavier, believing it to be too naive and shortsighted, Cable felt that it was his duty to carry on in his father’s stead. Now a member of Xavier’s brood, Cable and the X-Men continued their battle for mutantkind’s future.
After the passing months had healed the emotional scars, the wound of loss was ripped open for Cable and Phoenix by the arrival of Apocalypse’s former servant and chronicler, Ozymandias. Appearing through a teleportation portal in the Xavier Institute, Ozymandias beckoned the two X-Men to follow and learn the truth about their lost father/husband. Arriving in the ancient Egyptian’s sanctum, Cable and Phoenix learned that the unified creature of Apocalypse and Cyclops yet lived.
Ozymandias explained that he had sent a mutant named Anais to search for the lost Apocalypse, and had lost contact with her. Chosen for her devout dedication to Apocalypse and his vision, Ozymandias could only now assume that Anais had found her former master and was trying to aid him in a manner Ozymandias could only guess. Interested in a far different objective than Anais, Ozymandias told the two X-Men that he wished them to find their former teammate and pointed them to the African continent.
Wandering the seas of western Africa in whatever ship he could find work, Cyclops, or rather Scott Summers, tried to make sense of his life. Amnesiac and lacking his trademark mutant power, Cyclops had no way of knowing of his unholy union with Apocalypse, but nevertheless felt it. Haunted by daily nightmares, Cyclops attempted to fight back the dark impulses and desires that gnawed at his psyche. The evil that now lurked within the former X-Man, however, would not be denied.
During a brief encounter with Anais, Cyclops learned/remembered of an ancient place called Akkaba. Recognizing it as the place of his/Apocalypse’s birth, Cyclops made his way to Egypt, Anais and the two X-Men hot on his trail. Arriving in Akkaba, Cyclops was enchanted with the place of his birth, seeing not ruins but the magnificent city as it was five thousand years before. By the time Phoenix and Cable arrived at Akkaba, Cyclops was now more, by far, the being once known as Apocalypse. Easily besting Cable in battle, Apocalypse’s emerging personality seemed triumphant, until the gentle voice of Cyclops’ wife soothed his thoughts through their psychic rapport. Finally able to calm the beastly union of her husband and mutant overlord, Phoenix managed the impossible and psychically separated the two.
Now separated from his host body, Apocalypse was without shape or form, existing only in spirit. Seeing this vulnerability, Cable, whose entire life had been tortured by the menace of Apocalypse seethed in anger. Having recently adopted the spearlike Psimitar, a weapon through which he could focus his telepathic abilities, Cable approached the cause of most of the pain in his life, and struck. After five thousand years of terror, the being once called En Sabah Nur, was no more. [X-Men : The Search for Cyclops #1-4]