From this point on, Sinister seemed to adopt a less visible posture. He would only appear to point the direction that he felt the X-Men needed to go, or give them information that he needed them to know. During a vacation to Alaska to meet his family, Cyclops was approached by Sinister, who revealed the existence of the Legacy Virus, and how Stryfe had tricked Sinister into unleashing it into the world. It was also during this conversation that Sinister let slip the possible existence of an unknown brother to Scott and Alex Summers. [X-Men (2nd series) #23] (For more details on the mysterious third brother and the clues hinting at his identity, follow this link : Third Summers Brother) Sinister's interest in the Legacy Virus continued as he collected samples from infected patients while under disguise. [X-Men (2nd series) #27]
Sinister's interest in Cable did not end either. Time it seems, as Sinister always liked to say, was on his side. The various X-Men teams, X-Factor, and even X-Force all seemed to be on the lookout for Apocalypse. Cable himself still tracked his ancient foe. Sinister waited for any of the forces to do the job that he himself could not. On one occasion Sinister attempted to exacerbate the conflict between Cable and Apocalypse. Once again Sinister appeared before Cable to inform him of his past. On this occasion Sinister attempted to impart to Cable the scope of plans and events that Sinister set in motion that ended in Cable's birth. Sinister prophesized to Cable that it was only a matter of time before a final conflict between Cable and Apocalypse would ensue. As it was a necessity that Cable won in this conflict, Sinister offered to cure Cable of the techno-organic virus with which he was infected as a child. Ultimately Cable refused, but not before Sinister proved that when the time came, Cable might need Sinister's help. [Cable Annual '99]
As it turned out, the time of final confrontation between Apocalypse and Cable was swiftly approaching. For years, the prophecy of a group of mutants called The Twelve had circulated through the mutant world. In a swift series of moves, Apocalypse gathered twelve mutants together and plugged them into a central machine of Celestial technology. Apocalypse claimed that the entire prophecy was of his own design to lure twelve specifically chosen mutants together. Once assembled, he could channel all of their energies together and bundle then in his next host body to gain omnipotence. Unknown to Apocalypse, Magneto, one of the twelve he had chosen, had lost most of his mutant power. Due to this mistake, along with underestimating the power of another of his chosen, the Living Monolith, Apocalypse's plans began to fall apart.
Attempting to pull victory from defeat, Apocalypse began to merge with Nate Grey, the genetically engineered progeny of Scott Summers and Jean Grey from an alternate dimension. In a gambit to prevent that victory, Cyclops pushed Nate Grey away from Apocalypse's energy field, causing Apocalypse to be merged with him instead. The Apocalypse/Cyclops hybrid escaped leaving the fate of Cyclops in question. [The Twelve]
After a few months, evidence emerged of Cyclops being alive. Cable and Jean Grey tracked the rumors until the found Cyclops in Egypt, the land of Apocalypse's birth. At this time both halves, Apocalypse and Cyclops, were fighting for control of the body. Jean, using her telepathy, was able to separate the Apocalypse spirit from Cyclops. Cable using his telepathic powers focused through a weapon called a Psimitar dispersed the spirit of Apocalypse, effectively killing him at last. [X-Men Search for Cyclops #4]
After all of the machinations of Sinister to find the proper bloodlines, cross breed them to produce a powerful union and use that progeny as a weapon against Apocalypse, victory had been realized at last. Apocalypse was dead. Sinister no longer had a master.