Hey all so playing through Skyrim my first time and I've gotten to the Regain Winterhold quest for the empire and stumbled upon the Dark Brotherhood quest to kill the emperor. I'm assuming one ends the others questline? Is this true or can I kill the emperor for the DB and continue my Empire story line? Seems unlikely to me. Please avoid spoilers if you can!

Yes. Because they never know who the assassin was.

Just changes a bit of dialog in certain points, but nothing else changes. I tried it!

Thank you both for the quick replies.

I don't believe the Civil War quest line involves the Emperor himself in any way, so you should be safe.

It's bad for roleplaying purposes, though. But nothing changes, except dialogue a bit.

Yeah, my character was a Legion supporter who pledged herself to protecting the Emperor and Empire. I ended up having to head canon that she thought the Emperor was someone that just had to die.