Chapter V : The Gathering of Forces
After his brief reemergence in 1859, Apocalypse slept for another four decades. Emerging once again at the cusp of the 20th century, Apocalypse again enlisted the aid of his latest acolyte, Mister Sinister. Once again betrayed by Sinister, who infected his master with a techno-organic virus, Apocalypse sent him away, instructing Essex to never appear before him again. Aparently from the start, Apocalypse knew that Sinister had been trying to betray him, but had hoped that Sinister would change his mind and join his cause. Alone once more, Apocalypse returned to his regenerative hibernation. [Cable Annual ’99]
This second encounter with Sinister is the last known awakening of Apocalypse prior to the late 20th- early 21st century. However, as it is the way of Apocalypse to have his movements be covert and his actions subtle but never seen, it is not unlikely that Apocalypse could have resurfaced to see if the time was right for his grand scheme. In fact, there is evidence to show that he maintained control over at least one of his organizations, the Cult of the Living Pharaoh, an offshoot of his Children of the Sun organization. Having been formed thousands of years before, Apocalypse’s minions had kept track of the bloodline of the pharaohs and watched for one of special abilities. One such descendant arose when Egyptian citizen Ahmet Abdol manifested his mutant powers, slaying those whom he held responsible for the death of his wife. 
Appearing immediately thereafter in disguise, Apocalypse claimed to be a humble servant of the Cult, who believed that Abdol was their “Living Pharaoh.” Having already come to believe that he was indeed descendent from the line of ancient kings, Abdol quickly took to the role of Living Pharaoh, acting as lord and master of the cult. [Marvel Graphic Novel #17]
Though Abdol was now his pawn, En Sabah Nur needed to manipulate Abdol's genetic potential to transform him into the tool he would need in the future. Despite their previous history, the disguised Apocalypse employed the assistance of Mister Sinister to use Celestial technology to modify and increase Abdol's abilities by mixing his genetic material with that of Alex Summers, at the time still an infant from the powerful Summers bloodline Sinister had been grooming. This process inadvertently tied Abdol’s use of his own powers with that of Alex Summers, troubling Abdol for decades to come. However, this was of no importance to Apocalypse, who had his tool and only needed to wait for the opportunity to use it. [Uncanny X-Men (1st series) #376]
However, it seems he would soon slumber no more, for soon after an important temporal event occurred which would indirectly lead to his decision that the 
Time of Testing was imminent. At this point, some ten years prior to the formation of the X-Men and while hibernating in a hidden mountain fortress in Switzerland, Apocalypse was awakened by his equipment, which had detected an energy abnormality. Awakened almost a century earlier than he had planned, Apocalypse decided to examine the world and determine its conditions for testing. It is doubtful if Apocalypse ever learned the origin of the energy anomaly that triggered his awakening, but he no doubt would have been shocked to learn it was the arrival of his old nemesis, the Traveler. The irony would not have been lost on Apocalypse, however, as the Traveler, the man now called Cable, had journeyed back to prevent the ascendancy of Apocalypse, and instead had caused his emergence. [Cable #minus 1]
The next time of which we are certain of Apocalypse’s actions, ironically, had nothing to do with the emergence of mutants. After a confrontation with the hero known as Power Man, terrorist and global blackmailer Moses Magnum fell down a shaft which his laser drill had bored to the center of the Earth. [Power Man Annual #1] To Magnum’s surprise, he was saved from the fall by the teleportation device of Apocalypse. [Classic X-Men #25] Transformed by Apocalypse, Magnum continued his terrorist activities and, in doing so, did the bidding of Apocalypse by testing the strong and winnowing the weak. The first use of Moses Magnum’s new abilities and technology came during his assault on the isles of Japan, where he was confronted and defeated by Xavier’s X-Men. [X-Men (1st series) #118-119]
Unknowingly, the disciples of Xavier had just had their first encounter with the schemes of Apocalypse. As was his manner, Apocalypse worked in the shadows and used others to test the strong. The time was soon approaching when the ancient mutant would adopt a more direct approach.
It was a time shortly after the formation of an organization known as X-Factor by all five of the original X-Men that Apocalypse made his first public move. Apocalypse had gathered a group of mutants composed of Frenzy, Stinger, Time Shadow and Tower, all of whom called themselves the Alliance of Evil. Apocalypse had enlisted the reluctant aid of a mutant named Michael Nowlan, who had the ability to augment the mutant powers in others. Despite the addictive nature of Nowlan’s powers, Apocalypse planned to use them to provide mutant-kind with a source of unlimited might. Apocalypse would then lead this army of super-mutants in a war against all of mankind.
After a brief escape from Apocalypse’s chateau headquarters, Nowlan was recaptured by the Alliance. This abduction was witnessed by X-Factor, who followed the Alliance to its lair. During the ensuing battle, Nowlan and his wife were killed. His motive in the conflict now as dead as the Nowlans, Apocalypse abandoned the battle, as well as his disappointing Alliance of Evil. His latest pawns abandoned, Apocalypse gathered new pieces for his plan of pruning mankind and those mutants not fit to survive. From across the United States, Apocalypse gathered his Horsemen.
Before his planned attack on Manhattan was to begin, Apocalypse summoned X-Factor to his ship, the same Celestially constructed vessel he had acquired long ago. After explaining to them his intentions, he offered X-Factor a place at his side. It was a situation Apocalypse felt he could not lose. Should they accept, he would have new recruits in his operations. If not, they would try to stop his Horsemen and, in doing so, test them. Either way, they served the will of Apocalypse. Before his operation was to commence, Apocalypse showed X-Factor his newest recruit, someone of whom they were well acquainted.
During the recent massacre of the tunnel-dwelling Morlocks, Warren Worthington, also known as the Angel, had had his mutant wings so severely damaged that they subsequently had to be amputated. Having lost the most precious thing in his life, it seemed the Angel had attempted suicide by detonating an explosive while piloting a private plane. While the rest of the world, including his friends and teammates, believed him to be dead, Angel had been rescued by the teleportation machinery of Apocalypse. Offered a chance to have his wings restored, Angel had accepted a pact with Apocalypse and had become his fourth Horseman, Death.
During the ensuing battle, Death fought his former teammates. However, when tricked by Iceman into thinking he had killed his old friend, Death turned on his master. With Death/Angel’s help, Apocalypse’s Horsemen were defeated by X-Factor. Far from dismayed, Apocalypse did not consider it a defeat, but a victory of lesser degree. Division now existed with his former Horseman joining X-Factor while Apocalypse claimed one of their members, Caliban, as his new Hellhound. As X-Factor now controlled his Celestial ship, Apocalypse predicted that it would cause distrust between the mutant group and the New York human populace. And as for the battle itself, X-Factor had proven that they were among the strong. [X-Factor (1st series) #24-26]
Chapter VI : A Sinister Connection
As certain members of X-Factor would soon learn, Apocalypse was not alone in using them for their own ends. Since his betrayal of Apocalypse in the mid 19th century, Mister Sinister had plotted and schemed on his own. The goal of his experiments with genetics over the years was twofold. First, he wished to help unlock the genetic potential of mutants. Secondly, he searched for the optimum pairing for a union of unlimited power. This offspring, Sinister hoped, would be powerful enough to do what he could not: destroy Apocalypse. Over the past few years, Sinister had decided on the two mutants whom he felt could produce such an offspring, Cyclops and Jean Grey. His choice now made, Sinister allowed nothing to deviate him from his course, even the apparent death of Jean Grey, later revealed to be the Phoenix Force, on the Earth’s moon. Nevertheless, through a series of schemes and machinations that would have made Machiavelli proud, Sinister obtained the child of Cyclops and, more or less, Jean Grey: Nathan Christopher Charles Summers. [Uncanny X-Men (1st series) #201]
The entire saga of Sinister’s plan seemed to have come to a close during the conflict known as Inferno, where demonic creatures from the dimension of Limbo attempted to open a rift between the worlds and spread chaos. Nathan Christopher’s mother, Madelyne Pryor-Summers, in actuality a clone of Jean Grey, sided with the demonic forces and, by the end of the conflict, lost her life. Having learned of Sinister’s involvement, the combined forces of the X-Men and X-Factor tracked down Mister Sinister, confronted him and, apparently, killed him. Cyclops and Jean Grey recovered their lost infant and believed that, at last, their nightmare was over. Little did they know that the entire ordeal would gain the notice of their other great foe, Apocalypse. [X-Factor (1st series) #39]
After his most recent awakening, it is unclear if Apocalypse and Sinister had made contact with each other. It is certain, however, that Sinister would have attempted, at all costs, to keep Apocalypse from learning of his secret project. After the Inferno conflict, Apocalypse must have wondered about the nature of Sinister’s interest in the Summers’ child and possibly deduced a deeper motive to Sinister’s actions. A few months after Cyclops was reunited with his son, Apocalypse made a move of his own.
Over the previous few months, Apocalypse had gathered a mixed group of mutants and Inhumans, whom he called the Riders of the Storm. These Riders had the specific mission of testing mutants to see if they were fit to survive. Now, Apocalypse would have them test X-Factor. Under the power of a mutant called HardDrive, the Celestial ship X-Factor had previously claimed from Apocalypse lost all semblance of control. Rising into Earth orbit, the ship exploded violently. Through the help of the Inhuman royal family, X-Factor and their allies survived, but had failed in preventing Apocalypse’s Riders from abducting Nathan Christopher. Taken to the Moon by the royal family, they were informed that Apocalypse had seized control of the Inhumans’ lunar refuge, with the purpose of turning its populace into an army of conquest.
Now in control of young Nathan Christopher, Apocalypse had infected the toddler with a techno-organic virus. If the boy died, the threat would be over. However, if the child survived the process, Apocalypse foresaw a use for him (perhaps anticipating the final ceremony of the Gathering of the Twelve). As Apocalypse waited for his answer, X-Factor launched an assault on Apocalypse’s lunar stronghold. Once inside, X-Factor was defeated and imprisoned by the Riders in energy draining tubes. Taunting his captives, Apocalypse asked why they never thought to question what was his ultimate goal in winnowing out the chaff from the wheat, the weak from the strong…
Apocalypse’s plan was foiled, however, with the arrival of the Inhuman royal family. While X-Factor had attacked Apocalypse directly, the royal family had freed the captive populace of the Inhumans. Now freed, X-Factor and their allies defeated the Riders of the Storm, destroyed the energy draining machinery and seemingly killed Apocalypse. The victory was bittersweet, however, as it seemed that Nathan Christopher would soon die of Apocalypse's techno-organic virus. Cyclops' only chance to save his son came in the form of a woman from the future, who answered to the name Askani. Reluctantly, Cyclops gave his son to this woman, who claimed to have been sent back to protect the "Chosen One," which seemed to be the Summers baby. After a brief goodbye, Cyclops watched as his son was transported through time, apparently never to be seen again. [X-Factor (1st series) #65-68]