Did I screw up the Bloodmoon DLC? (spoilers.)

[Yuki Nagato]

I did all the Raven Rock quests. I sided with the East Empire Company, and at the end of the quest the Imperial Captain Carius attacks you and you have to kill him.

Then I found out that he's the one you have to talk to in order to continue the main quest with the warewolves (Which I haven't even started yet)

Am I screwed?

UPDATE:

somehow I didn't realize until now there were 2 quest givers in the fort with nearly identical names. Everything is going along nicely now.

[Doggy Friend]

I did all the Legion quests in Fort Frostmoth before completing Raven Rock quests and never got attacked by Captain Carius.
You might consider loading a save just before completing Raven Rock line and do Legion first as well.

[Yuki Nagato]

Originally posted by IT Traveller:

I did all the Legion quests in Fort Frostmoth before completing Raven Rock quests and never got attacked by Captain Carius.
You might consider loading a save just before completing Raven Rock line and do Legion first as well.

Yep, I'll try that. I didn't even know there were leigon quests until after I looked on the wiki post-killing him.

Oh well, I didn't really do much in the meantime.

[Valden21]

Bloodmoon has two questlines; the main questline, and the East Empire Company questline. Both questlines begin in Fort Frostmoth. The EEC questline has two separate branches to it, depending on which of its two quest-givers you ally yourself with. BUT, Captain Carius isn't one of them, and both branches have the same final boss; it isn't Captain Carius. You only have to kill him if you make one specific decision late in Bloodmoon's main quest. If you go one way, Captain Carius becomes an enemy; if you go the other choice, he's an ally.