(Possible) Idea for Emil's death:
Emil faced a test during his retreat from Terra, to join Chaos or refuse and accept his ship AI's help. Both those possible futures influenced him, and everything got all fucky when you blend (A Shitload of Culexii) + (The Gods) + (Abominable Intelligence) + (A Very Powerful Psyker) all into the same cubic kilometer of space and time. Timelines fractured and blended together.
Emil passed. And Emil failed. Like a particle-antiparticle pair, when Emil rejected the Gods they still took the psychic resonance/impression of now-matured Emil with them back into the Warp. Where they kept his four biological limbs, shorn off as an infant.
One Emil returned to his Legion. And one Emil began to take on new life within the Maelstrom, growing like a cancerous tumor within the Warp. Many years passed before the original Emil began to learn of his opposite waging slaughter across the cosmos, raising a Warp-infused Astartes army in blasphemous imitation of the Steel Souls.
Callously, Emil lets Anti-Emil rampage among Imperial forces for a while, but eventually the two must inevitably meet and in doing so _____ happens.
The loop closes, and it is shown that even such a sacrifice as tearing off your own arms and legs cannot fend off the inevitable dying of the light forever.
Possible plot threads:
The Emperor tips the scales at the last second to stymie Chaos just a little. Emil dies, but at the very end is relieved to know that he was wrong about the Emperor abandoning him.
If we go for maximum grimdark, the Steel Souls themselves are also wiped from existence during the final struggle.
They DON'T annihilate each other, but rather begin an endless back and forth campaign across the Galaxy, destroying all in their path to try and gain an edge over their foe, ignoring all else.
Their psychic struggle feels a little too much like the War In Heaven, and the Eldar/Necrons are drawn in somehow.
Thoughts?