The horrific result of "The Twelve" (both from a story and quality standpoint) had Apocalypse and Cyclops merging into... Cyclopalypse. But not all was well for Apocalypse, as he still wanted to draw on the power of the remaining 11 mutants to ascend to Godhood. So, he uses his abilities over time and space - which, he somehow managed to absorb from Bishop and Mikhail for reasons unexplained - to move the Twelve into alternate realities and trick them into discharging their powers to fuel him.
While the twisted take on the first issue of X-Men and a peak at 100 years into the future are pretty neat, they're hurt by the fact that the concept makes zero sense. If Apocalypse can rewrite history, he can simply make his experiment successful. No fuss, no muss.
There are also issues - like a reunion of the New Fantastic Four (Wolverine, Spider-Man, Ghost Rider and Hulk) - that serve no purpose to the context of the story, as entertaining as that particular example may be. Their existence is also a mystery because they have no effect on Apocalypse's actual plan. Perhaps he got bored and wanted to be entertained for a while. Making things worse is how the X-Men are all played for fools and are continuously naive. By the time you get to Jean Grey's sob story over seemingly losing her husband, you don't care.
It's with that feeling that we go into "The Search for Cyclops." Faced with that uphill battle, it manages to fall backwards before making a tread on the incline.
Scott is somewhere in the Middle East fighting amnesia (ARRRRRRRGH!!!! Trope) unaware that he is BOTH the stalwart X-Men original AND evil incarnate. Over the course of a grueling four issues, Jean and Nathan track him down despite the meddling of additional parties and finally put the Scott Summers/En Sabah Nur "partnership" out of its misery. Status quo restored. I know some people dislike it when that happens, but in this case how can anyone possibly argue against this decision?
Cyclops merging with Apocalypse would go on to have consequences, though, in ways the reader would never expect. And it's all thanks to to one man who gave the X-Men franchise the kick in the ass it needed so badly at the turn of this century.
Enter: Grant Morrison.