Complex sentence: Magneto and Mystique had been assisting Apocalypse under the false pretense of Apocalypse using the Axis to create an alternate future where Earth was ruled by mutants: upon learning his true plot, they turned on Apocalypse and Mr. Sinister and helped the X-Men to stop him.
Split into simpler sentences: Magneto and Mystique assist Apocalypse under the belief that Apocalypse is using the Axis to create an alternate future where Earth was ruled by mutants. Upon learning his true plot, they turn on Apocalypse and Mr. Sinister and help the X-Men to stop him.