This is exactly where I see this going; Apocalypse certainly has been shown a lot in the opening credits.
I could see the finale being a loose adaptation of both Fatal Attractions (with Magneto going berserk on humanity, ripping out Logan’s adamantium and all) and Evolutionary War, with Apocalypse taking the High Evolutionary’s role.
After “Beyond Good and Evil”, Apocalypse is revealed to have survived his fate at the Axis of Time and has rededicated himself to guiding and enhancing the evolution of humanity so that his race may one day be supreme to all others, including a race known as Beyonders. To this end, he ordered Sinister to hack Master Mold and decimate Genosha, knowing it will ignite war to accelerate Earth’s evolution and eliminate perceived threats to genetic purity so that he (and Sinister’s science) can make the perfect race—in line with his ‘survival of the fittest’ mantra. Their first attempt at this was Nathan Summers, but the X-Men interrupted them (and Apocalypse unknowingly created his greatest enemy).
Bishop specifically said in Episode 2 that’s he’s never heard of a future where Magneto led the X-Men. I think we’re gearing up Apocalypse’s return & an Age of Apocalypse adaptation in Season 2…