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Nightmare Fuel: Age of Apocalypse
A lot of the imagery is truly horrific.
The original comics contained a map of what Earth in the Age of Apocalypse looked like. Large swaths of the planet were irradiated waste lands, and Central America was non-existent due to nuclear bombing.
The entire Generation Next series sits at the top of the whole cross-over in this regard. From Colossus' sadistic teaching methods, to graphic depictions of an extermination camp where Muggles are worked to death, to a number of gruesome deaths befallen by both heroes and villains alike, this was extremely disturbing stuff for Marvel Comics of that era.
Made especially jarring since the regular Generation X was one of the more lighthearted X-Men titles.
The sea full of rotting corpses where culled humans had been dumped.
One comics opening scene is Bishop literally climbing hills of corpses...