So here's the scenario. There's another species with a very alien mindset and completely different world view. Perhaps they're an insect hivemind or perhaps they're militant conservationists and live in tune with nature.
Essentially our mere existence they see as a threat due to consumption, reproduction etc. Whatever the reason. Maybe they're just Vulcans that logically see humans as a threat to every other species merely by existing.
In any event they either want to drive humans to extinction or at best limited to an island or something similar. Extinction might be in the traditional way or just banning humans from reproducing in some way.