Looks like they're going to be adapting Lifedeath 1 and 2 (Uncanny #183 and #198, respectively). Both stories took place after Storm lost her powers because of a government weapon that neutralizes mutant abilities.
Someone already pointed out that Magneto's fit in this series is taken straight from X-men #200 (the Trial of Magneto).
The season finale title (Tolerance is Extinction) might be a reference to the X-tinction Agenda story arc in 1990, where the X-men were captured and taken prisoner in Genosha, resulting in a huge crossover between them, X-factor, and the New Mutants versus Cameron Hodge and the Genoshan Magistrates.
If only Jim Lee could have done this entire crossover. That Wolverine vs Archangel fight