Black Omen in 1000 AD -> Beat Lavos 1st form -> Portal Out
Black Omen in 600 AD -> Portal Out
Black Omen in 12,000 BC -> Finish Him

If you clear the Black Omen in the later time periods it is still there in the earlier ones. (Just most of the bosses are already dead.) But you can fight Queen Zeal three times and have Ayla steal stuff every time.

As for endings, I dunno. Save just before the fight and watch all three.