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The plot as I remembered is as follows:
Cable's children dies and he travels back in time.
Apocalypse prepares some sort of a disease, which will eventually kill Cable's children.
Cable destroys the virus caches and infects Wolverine. A serum is developed thanks to Wolverine's immune system.
Do you know which episodes fall into this arc?
You're describing the X-Men: The Animated Series episodes Time Fugitives (Part 1) and Time Fugitives (Part 2).
Cable and Clan Chosen are fighting Apocalypse and his robots in the year, 3999 AD until a temporal storm devastates the city. Cable questions his A.I. about what's happening and it explains how Bishop travelled to the past and stopped a disease from spreading, meaning mutants would die. It further goes on to explain hoe Cable's timeline is going to cease to exist.
Back at the X-Mansion, Beast examines Wolverine and finds that he has fully recovered from the plague, providing the anti-bodies Cable needed to save his timeline. Cable returns to his timeline to find that everything is restored to as before and Tyler is safe.
