The baby that Cyclops and Madeline Pryor (Jean Grey’s clone) have is Cable, a weapon devised by Sinister to take out Apocalypse. Apocalypse is in fact responsible for the child having to be sent into the future as he infects him with a techno-organic virus; a condition which can only be treated thousands of years from now.
When the future and now frail Apocalypse learns of the child’s presence in his time – this time travel stuff sure is confusing, huh? – he tries to steal Cable’s young body for himself, but ultimately fails. As it turns out, a clone of the young Nathan Summers had been created just in case he succeeded, and while the original grows up to become the warrior Cable, his clone grows up to become the mutant terrorist known as Stryfe. He then goes on to be responsible for creating The Legacy Virus, which wipes out countless mutants.