"Two years after the Yeerk defeat Jake finds work training a morph-capable counter-terrorism unit created in response to a spate of attacks on alien tourists. Apparently some of the worst are perpetrated by cults that think the presence of aliens on Earth is staving off a long-awaited apocalypse."
-TVTropes
Wait, is the future of this world basically XCOM: Chimera Squad
Actually yes I do appreciate that the ending isn’t a happy one