To tell the truth...
Be it the God Emperor or the Abyssal Race in general...
They never really stood a chance.
Don't be mistaken. The Abyssals are extremely strong. They are probably the most fearsome race to ever exist in the entirety of the Outer Worlds and they didn't became strong through luck, they reached their current state by relying to their own craft and smarts.
Nobody could match them on a head-on clash, they're are that strong. And if their power continues to grow this way, they will truly become the rulers of everything.
Unfortunately, they got too absorbed in their own ways. Got so drunk in power that they've become careless. In addition to fate playing games with them, in the end they met their downfall.
They would've imagine that they invoked the ire of something they could never hope to match.
