Chapter VII : Sins of the Future
As before, whenever exhausted or injured, Apocalypse returned to his regeneration chamber for hibernation. To his surprise, before his cycle was complete, he was reawakened by his Riders. When the enraged Apocalypse demanded to know why he was revived in a weakened state, the Riders’ leader, Gauntlet, informed Apocalypse of recent events. Apocalypse’s Horsemen had kidnapped Cyclops and Jean Grey, supposedly under his instructions. Further, Charles Xavier, mentor and founder of the X-Men, had been the victim of an assassination attempt, reportedly perpetrated by the man called Cable, the leader of the recently formed X-Force. These incidents, combined with Apocalypse’s burning need to determine their meaning, began the conflict that would be referred to as the X-Cutioner’s Song.
After a brief conflict with the X-Men, Apocalypse desperately needed another regeneration cycle and headed to his temple base in Bani Maza. Once again, his hibernation was interrupted, but this time by the mutant terrorist known as Stryfe. Using his prodigious telekinetic powers, Stryfe easily bested Apocalypse and the Riders in attendance. Gloating over the ancient mutant, Stryfe rambled continuously of crimes that Apocalypse had perpetrated against him. Telekinetically tossing him around like a rag doll, Stryfe accused Apocalypse of causing millions to cry out in agony, which compared little to the cries of a lonely child.
Apocalypse managed to make his way to his teleporter and escape, but in his departure, he lost his Riders. Having been indoctrinated to follow strength, the Riders of the Storm, now calling themselves the Dark Riders, changed allegiances to Stryfe. Stryfe, having defeated their master, now became their new one. But who was this mutant, who so easily defeated Apocalypse, formerly the mightiest of mutants? Why did he hate Apocalypse so, and what crimes had Apocalypse committed against his person? The answer lay not only in Apocalypse’s recent past, but in his far future.
During the recent confrontation with X-Factor on the moon, Apocalypse had infected Cyclops’ son, Nathan Christopher, with a techno-organic virus. After Apocalypse’s defeat, Nathan Christopher lay near death until the time-traveling mutant named Askani promised to take the toddler into the future, where he could be cured. Reluctantly, Cyclops had consented and Nathan was taken into the time-stream. 
Although Nathan survived the journey, his guardian, Askani, did not. Upon arriving at her time period, the 38th century, her body lost coherence and she died. The Mother Askani, in actuality Rachel Summers, another child of Cyclops from another timeline, was the leader of the group, also called the Askani. Worried that her doctors would be unable to save her “brother,” Mother Askani ordered a clone to be grown from Nathan’s uninfected cells. Miraculously, both clone and original survived. However, moments after the operation’s success, the future Apocalypse’s Canaanite troops attacked the Order of the Askani’s stronghold. The cyborg kinsman Boak was able to retrieve young Nathan from his tank, but couldn't reach the clone before he had to flee. Therefore, the virus-free clone was captured by Apocalypse himself. [Cable (2nd series) #7-8]
The young Nathan Christopher had been taken into the future, but not the same future as the one from which Rama-Tut originated. Rama-Tut’s future was in the 30th century and was an idyllic utopia. This future was in the 38th century, and was a hell on Earth. For some time, Apocalypse had gained control of the entire planet. He had set up a brutal Darwinian aristocratic system and mutants were the ruling class. The ideology of “survival of the fittest” which Baal had taught his adoptive son seven thousand years before was the creed of the land today. However, although he was still the strongest of the strong, Apocalypse’s might had weakened considerably.
Most likely starting after his resurrection by the Celestial ship in the 12th century BC, Apocalypse had been forced repeatedly to enter a state of hibernation in regeneration chambers. During the battle with X-Factor in the city of the Inhumans on the moon, Apocalypse had admitted that he needed the life essence of others to sustain himself. Now, two thousand years later, his weakness had only grown even greater. Bio-armor, which he had been wearing by his encounter with Nathaniel Essex in 1859, had grown ever more important and, unfortunately for Apocalypse, far less reliable. [X-Men: Phoenix #1]
Seeking out a host body that could sustain him for millennia, Apocalypse’s forces had captured the infant clone of Nathan Christopher at the Order of the Askani. Recognizing the youth’s immense potential, Apocalypse raised the boy and named him Stryfe, after an old foe he had encountered in the 20th century. As the boy’s powerful mental abilities began to emerge, Apocalypse taught him in their optimum usage. The ancient schemer would need Stryfe’s abilities mastered before trying to inhabit the body. The time of bonding eventually came but, to Apocalypse’s surprise, the procedure failed. To Apocalypse’s horror, the boy was a clone and thus unsuitable for use as a host. Adding to Apocalypse’s ills was the arrival of a trio of rebels, Slym, Redd and Nathan Dayspring.
During the battle with Apocalypse’s forces where the clone of Nathan Christopher had been captured, the Mother Askani had been severely wounded. Realizing that she would not be around to raise the Chosen One, Mother Askani telepathically reached back in time and summoned Cyclops and his wife, Jean Grey-Summers, just days after their wedding. Placed in cloned bodies that resembled their originals, Cyclops and his wife adopted the aliases of Slym and Redd Dayspring. Given a second chance to raise the child that they had lost, “Slym” and “Redd” spent the next twelve years raising Nathan “Dayspring” and instructing him on the use of his emerging mental abilities. After joining a small resistant force, the trio had learned of the clone in possession of Apocalypse and his intention of using it as a host body. The trio managed to stealth their way into Apocalypse’s fortress during the attempted bonding process. When the bonding failed, Slym, Redd and Nathan attacked, preventing Apocalypse from bonding with anyone else. Separated from any useful host, Apocalypse perished. Shortly thereafter, the aged Mother Askani too perished. Without her power, Scott and Jean’s minds returned to their original bodies in the past, only hours having passed there. [Adventures of Cyclops and Phoenix #1-4] During the Gathering of the Twelve in the modern era, Apocalypse first attempted to transfer his essence into a new living host, another child of Cyclops and Jean Grey called Nate Grey from the Age of Apocalypse. He failed, and according to some sources those events marked the final division of Cable's timeline from Earth-616. Therefore, it's unknown if the Apocalypse of Cable's future was successful in claiming Grey as a host, or perhaps making the same mistakes by trying to claim another Summers as his host in this future. [X-Men (2nd series) #97]
Chapter VIII : The X-Cutioner’s Song
Even with the death of the malevolent Apocalypse, things did not especially improve over the next several years. The New Canaanite government took over after Apocalypse and continued his mutant-led aristocratic policies. Stryfe, considering himself the heir apparent to Apocalypse, attempted to conquer the planet back with his group the Scions of the High Lord, while Nathan Dayspring and his rebel Clan Chosen were fighting for peace and coexistence against both Canaanites and Scions. Finally, both Nathan and Stryfe failed when the Canaanites established full global control. Stryfe, refusing to acknowledge defeat, traveled back in time to exacerbate the mutant uprising at its early years. 
Not considering the battle finished, Nathan decided to follow his foe and, arriving in the late 20th century, at this point adopted the guise of Cable. While Cable recruited the leaderless New Mutants and transformed them into X-Force, Stryfe had formed a worldwide terrorist organization called the Mutant Liberation Front, or the MLF. [X-Force (1st series) #17]
Some of the earliest missions of the MLF were the thefts of several ancient artifacts. These artifacts were all ancient art and jewelry depicting the many past appearances of the ancient being Apocalypse. While sewing the seeds of chaos in the past, Stryfe was determined to have his revenge against the monster who had wished to use his body as a host. Time would pass, but, eventually, Stryfe got his wish.
After a chance encounter with the enigmatic Mister Sinister, Stryfe struck a bargain. If Sinister could produce Scott Summers and Jean Grey, upon whom he also wanted revenge for abandoning him as an infant, and bringing Apocalypse into the open, Stryfe would give Sinister a unique prize; a canister containing the genetic material of the Summers family line covering the next two thousand years. Apparently recognizing Stryfe for the union between Cyclops and the clone Madelyne Pryor, Sinister accepted. Shapeshifting into the appearance of Apocalypse, currently in hibernation, Sinister enlisted the Horsemen of Apocalypse to capture Cyclops and Jean Grey, whom he them turned over to Stryfe. Stryfe, meanwhile, shed his bulky uniform and, impersonating Cable, attempted to assassinate Professor Charles Xavier.
The conflict now known as the X-Cutioner’s Song begun, Stryfe confronted Apocalypse, who had emerged early from hibernation to determine who had instructed his Horsemen to kidnap the Scott Summers and Jean Grey. Tracked to his hidden base at Bani Maza, Apocalypse was attacked by Stryfe who quickly defeated him. Apocalypse managed to escape and, unbelievably, joined forces with the X-Men, X-Factor and X-Force, the group Cable had recently formed. All of the pieces were beginning to fall into place with this complicated puzzle. The disciples of Xavier agreed to join forces with Apocalypse long enough to defeat Stryfe and recover their kidnapped teammates. It was Apocalypse who cured Charles Xavier of the affliction he suffered from Stryfe's assassination attempt. The conflict came to an apex at Apocalypse’s old base on the Moon. Wanting to put an end to Stryfe's madness once and for all, even though it meant his death, Cable activated a self-destruct and time-flux generator at the same time. In the resulting explosion, he and Stryfe were scattered through time, apparently killing them both. [X-Cutioner's Song]
The X-Cutioner’s Song ended without much finality. Cable would turn out to be very much alive in the future and would make his way back. During the conflict, Scott and Jean were lead to believe by Stryfe that he was their son, taken into the future. His bold lie would be revealed when, after returning from the future, Cable was told the truth by none other than Mister Sinister. [Cable (2nd series) #6-8] Sinister himself was cheated in his deal with Stryfe, as the cannister of genetic material would be revealed to be apparently empty. Worse, in truth it contained the deadly Legacy Virus, designed by Stryfe in the future to act as a doomsday weapon against all of mutant-kind. Unleashed in the past, it threatened the lives of all mutants worldwide. Over the next year or more, it would claim the lives of dozens of mutants, both friend and foe.
Apocalypse, it seemed, had died. His two recent attempts at regeneration interrupted, Apocalypse was low on the life-energy that sustained him. As the battle raged between Xavier’s forces and Stryfe, Apocalypse was beaten severely by his former vassals, the Dark Riders. Although he triumphed, Apocalypse was not long for the world. He asked Archangel to kill him, but his former Horseman refused, leaving Apocalypse to die, weak and alone. When the conflict was over, Apocalypse, it seemed was no more. With the apparent death of Apocalypse and Stryfe, the Dark Riders continued their mandate of testing the strong, though leaderlessly. The Riders would soon find a new mutant to follow, Cable’s son, Tyler. Believing he had been betrayed by his father in the future, Tyler had traveled back in time as well. After operating for a while under the guise of international arms dealer Tolliver, Tyler had recently adopted the name of Genesis and considered himself the new heir of Apocalypse, at least in spirit. During his first outing as the Dark Riders’ leader, Genesis confronted Cable and a few of the X-Men in a former stronghold of Apocalypse located in Akkaba. At the conclusion of the battle, the fortress lay in ruins and the two competing factions went their separate ways. After they had all departed, however, from beneath the rubble, something stirred. [Cable (1st series) #17-19, Wolverine (2nd series) #100]