Originally Posted by Ferlion

It's obvious he isn't dead.

Spoilers

Look, he's still alive, but severely weakened after the Jedi battle. The temple is about to cave in, you get a message telling you to get out of there, and you run. That's it. You are outta there. You don't stop to kill him. You leave him.

Then, literally the next time your on your ship (if Kira is all "ohh, I want your sexy body) you get a companion quest saying Children of the Emperor are receiving mental commands from him.