Actually, Morrison was continuing from the most recent previous writer, Scott Lobdell, who was cuing off a storyline by the great Alan Davis. In X-Men No. 98, Cyclops was thought lost, having been forcibly merged with Apocalypse. Cyclops was missing from the book for a year, until Jean Grey and Cable finally rescued him in the Search for Cyclops mini. Having spent so much time trapped inside Apocalypse, Scott emerged a much darker character, as shown in a brief run by Lobdell just before Morrison took over. In fact, there's also a subtle thing with the art: Before the Apocalypse storyline, Cyclops always used a gold visor. Ever since, the darker Cyclops has used a dark gray/silver visor.

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Cool. Didn't know that. I quit X-Men right after Paul Smith left and didn't return until Morrison.