Together with Martin and Jauffre (if he survived the battle for Bruma) you'll agree that you have to go to Imperial City and declare Martin the new Emperor. Go to palace.
Chancellor Ocato will immediately declare his obedience, but his speech will be interrupted by a guard, who tells everyone that the city is under attack. Gates of Oblivion are opening all over the place. You have to escort Martin to Temple of the One. This time the Emperor won't be following you - it's you who'll have to wait for him.
When you're in Temple District, it turns out that Mehrunes Dagon himself walks upon the earth! It means that crowning Martin won't do the thing any more, as barriers between Tamriel and Oblivion have been breached. Martin tells you that you have to go to the temple with him. Dagon stands before you, but surprisingly it's enough just to walk by him (lol). Enter the temple and watch what happens. We bet you're as disappointed as we were when it turned out that we don't get to kick daedric prince's but ourselves. Martin will sacrifice his life, do some weird stuff with the amulet, and transform into a dragon. After a short struggle both Dagon and Martin will be gone, thus ending the Third Era etc. Well, congrats.
After the battle you will be approached by Ocato, who'll give you the title of Champion of Cyrodiil and inform that an Imperial Dragon Armor is being prepared for you. It will be ready in two weeks.
Well, that's pretty much the end of the most important quest of the game. Fear not, though, as there is still a LOT for you to do. There are hundreds of dungeons, tens of quests, thousands of characters, all just standing there and waiting for you to come and see them. We'll help you, of course. Soon.