Here's what I'd do.
X-Force (2016) - Stryfe as the villain along with the Dark Riders working for Apocalypse
X-Factor - Sinister as the villain trying to stop Apocalypse by harvesting mutants' DNA to build an army of super soldiers
Uncanny X-Men - X-Tinction Agenda storyline with Cameron Hodge as the villain running mutant death camps in Genosha. Hodge's pure hatred pushes Apocalypse over the edge to the point where he declares war on humanity
Crossover - A mixture of Endgame, The Twelve and Apocalypse Solution.