Meanwhile Genesis (Tyler) had started to see himself as the rightful heir of the apparently departed Apocalypse. He ordered the Dark Riders to capture both Cyber and Wolverine, as he wanted to use Cyber’s adamantium to infuse it into Logan, and after brainwashing him, make him the new Horseman Death. Yet during the process, Wolverine’s strong will rejected the adamantium, which was expelled from his body as shrapnel, instantly killing some of the Dark Riders. Wolverine became a feral, noseless savage, and in a berserker rage killed most of the other Dark Riders and Genesis. [Wolverine (2nd series) #93-96, 99-100]
Despite the Time-Displacement Core being at the ocean bottom, Cable registered an alarm of somebody breaking into it. Together with Bishop, he investigated and they found Sinsear within the module, trying to get back to the Askani future. Cable knew that the core was unstable and wanted to stop Sinsear, but during their battle the machine got even more damaged to the point, where somebody needed to deactivate it from within at the cost of his own life. Cable felt responsible and was about to enter, but surprisingly Sinsear knocked him out and took his place. He managed to contain the timewave energy charge, thus saving earth, but Sinsear’s atoms were scattered across everywhen in time. [Cable (1st series) #41]
When Blaquesmith did not act as the nearly insane Sanctity ordered him from the future, she chose to send another disciple to make Cable do her bidding. To ensure that this time the operative would not rebel against her orders, she chose a very young boy, and placed him ca. 30 years in the past before Cable ever arrived in the present. This boy, named Ch’vayre, grew up at a secret monastry in the swiss alps, frequently visited by astral projections of Sanctity, tutoring him and reminding him of his mission. Over time he grew up to manhood and organized a local sect of Askani followers, telling them stories about the dark future, if his mission would be a failure. Apocalypse was responsible for the Askani timeline and Ch’vayre’s task was to engineer the final confrontation between Cable, the Askani’Son, and Apocalypse. 
Finally he thought the time was right and contacted Sebastian Shaw of the Hellfire Club, offering him very advanced technology, located at one of Apocalypse’s strongholds. The plan was to have Cable hunt down Shaw and Donald Pierce while they break into the stronghold, which certainly would have alerted Apocalypse. However the plan failed, as the ancient egyptian did not show up. Cable faced the two members of the Hellfire Club, who expected their supposed ally Ch’vayre to help them. Yet Ch’vayre did not want to let the villains get to the advanced technology and opposed them. Shaw saw this as betrayal and locked Ch’vayre away in one of Apocalypse’s hibernation chamber. Meanwhile Cable had been able to defeat Pierce, but the stronghold was going down. Cable established a brief telepathic contact with the trapped Ch’vayre before the base exploded. [Cable (1st series) #42-44, 51-53]
About a month after his disappearance, Blaquesmith was seen again, as a captive of Rama-Tut. The Pharaoh’s time machine malfunctioned but Blaquesmith told him that it was beyond repair. From his prison Blaquesmith telepathically contacted Cable to tell him that he needed to focus on his original mission, the battle against Apocalypse. Through their mental contact Cable learned of the base’s location and went to Egypt to rescue his old friend, against Blaquesmith’s orders who considered his own well being unimportant in comparison to the evil of Apocalypse. While they escaped from Rama-Tut’s headquarter, Cable was struck by a wave of mental energy, an effect of the Psi-War (a battle between Psylocke and the Shadow King that ended with a temporary worldwide loss of psionic powers). [Cable (1st series) #54-57]
Blaquesmith’s diagnosis revealed that though Cable could not use his abilities there was still some psionic activity in his brain, he only needed something to focus. Blaquesmith knew that such an object could be found with the Askani cult that Ch’vayre had established, so he sent Nathan to one of their temples on a small greek island. Once there Cable was attacked by the cultists, but the battle ended when they realized that he was the Chosen One that Ch’vayre had been lecturing about. They handed him a powerful weapon from the future, a so called Psimitar, able to focus and amplify psionic energies. Only brother Ceasar, the sect’s leader, was doubting Nathan’s identity, especially after Cable disbanded the cult, telling them that it would be his destiny to fight for a better future, not theirs. Ceasar was angry that years of study under Ch’vayre should have been in vain. [Cable (1st series) #58] Soon afterwards Cable’s abilities returned, but he kept the psimitar to focus his psi-powers through it.
All over sudden Stryfe returned fully alive and well without explanation, despite the fact that he was shown to be in hell earlier on. [X-Force #74] Together with X-Man Nate Grey, Cable at least prevented him from conquering Latveria (and Dr. Doom’s time machine), but his evil clone escaped once more. Cable and X-Man were lucky to survive the encounter. [X-Man #46-47, Cable (1st series) #63]
Once, Cable was abducted by people of a nameless dimension, apparently existing out of time. They had captured Madame Sanctity and planned to execute her, as her insane manipulations of time could not be tolerated any more. 
Cable knew that she was mad and could not be trusted, still he couldn’t simply stand by and allow the woman to get murdered. He defeated the people of the nameless dimension in a fair duel and both he and Sanctity returned to the points in time where they had been plucked from. [Cable (1st series) #69]
Ceasar’s anger developed into such hatred that he came to New York and took Cable’s girlfriend Stacey Kramer hostage, blaming Nate for taking away the only purpose he had had in life. Cable quickly disarmed Ceasar, but he could not prevent him from blowing apart the building in a last final attempt to hurt the Chosen One. [Cable (1st series) #70]
Finally Cable’s destiny was about to occur as the Twelve Saga loomed on the horizon. From the Askani future timeline, Rachel sent a message revealing the Twelve’s identity to Cable and also she arranged for him to visit an alternate timeline where the Twelve had failed and mutantkind‘s future was not a happy one, to explain the importance of the upcoming battle. [Cable (1st series) #65, 71]
Still before Cable could even think of gathering the other members of this group, he was captured by Apocalypse’s forces and the others ended up captive as well. It turned out that actually it was a faked legend started by Apocalypse himself to lure these mutants all into one spot. He wanted to combine the Twelve’s energies and transfer them into his next hostbody to gain omnipotence, yet the mutants could break free. In the end Cyclops made the ultimate sacrifice, as he pushed X-Man out of the bonding device, though now Apocalypse merged with him instead. [The Twelve]
With Apocalypse not gaining the Twelve’s powers, history was changed and the entire Askani timeline was erased from existence. While Jean, Scott, Cable and other people, who spent some time there, still remember it, it did not happen for Rachel, who is an chronal anomaly. She wound up somewhere else in the timestream; probably because her (dead) body was still in that future timeline in the instant it ceased to be. Rachel retains some pale memories of her life as Mother Askani, but that‘s all. She was hurled through the timestream towards the end of all time, and halfway through she felt the Phoenix Force abandon her to reasons unknown. She washed up on an apocalyptic world, and was held hostage by Gaunt, a man who had been imprisoned there for his crimes. She mentally contacted Cable for help and he traveled after her to save his sister. Cable challenged Gaunt to a duel to decide the fate of Rachel and emerged victorious, returning Rachel to the present with him. Rachel preferred that her return was kept secret from everyone else including Jean, while she tried to get resettled and attempted to lead a normal life. [Cable (1st series) #84-86]
Over six month after the merger, Cyclopalypse appeared again. Although the X-Men had believed Cyclops gone forever, he was still struggling with Apocalypse over dominance over their joined body. As various clues pointed to her husband still being alive, Jean embarked with Cable on a search for him. When they found the merged individual, Jean used her psi-bond with Scott to drag out Apocalypse’s essence and Cable disrupted it with his Psimitar, finally killing the millennia old villain. In the meantime Blaquesmith had hired mercenaries to kill Cyclopalypse, as he found the idea of them getting split or Apocalypse gaining dominance to dangerous. When Cable found out that his mentor had wanted to kill his father, he could no longer trust Blaquesmith. [X-Men Search for Cyclops #1-4]
Returning to the X-Men, Cable found that the mansion had been attacked by Stryfe. The villain wanted to explore Bishop’s energy absorption power to get hold of the Bete Noir, an energy entity trapped within earth’s core, as old and powerful as the Phoenix Force. Cable hunted Stryfe and wanted to kill him to end his crimes once and for all, placing Gambit and Bishop in the moral dilemma that they couldn’t allow cold blooded murder. Yet when Bishop no longer could contain the Bete Noir, Stryfe saw his error and sacrificed his own life to keep it from breaking out of it’s prison. The X-Men were left behind wondering if one final act of goodness could redeem an entire lifetime if evil. [Gambit & Bishop #3-6]
Shortly afterwards Cable and Blaquesmith parted ways while on the run from some villains. Blaquesmith was in a car that crashed into the Hudson River and hasn’t been seen since then. [Cable (1st series) #91-92]