Not sure which speculation thread to dump this in but here goes:
1. Aldudagga has Lorkhan and will-be-Dagon stealing bits of the Kalpas.
2. Presumably to make Mundus.
3. Sticking all the stolen bits of the Kalpas back someplace to prevents Alduin from ending it. Too much too eat to fill his stumach.
4. Mehrunes was made to get all the stolen bits back so the Kalpa could end.
5. Alduin is comming back now. So all stolen bits have been returned.
So what were these stolen bits and how were they destroyed?
Presumably bits of Lorkhan, or rather bits of his essence. He's always been a bit odd for the son Padomay. He's always been more then the Daedra, he was able to present himself as an Aedra to other Aedra. So what if Lorkhan stuck those bits of stolen Kalpa onto himself to be more, to be both?
Now his essence is gone or destroyed, both his Heart under Red Mountain as well as the Amulet of Kings. So Alduin can continue eating the world.
Probably needs a fact check.
edit:
There has been an idea floating around that in all the previous games Lorkhan was being liberated from his imprisonment in Mundus. What if he wasn't being freed, but rather destroyed entirely?
Or both?
edit:
I also hope someone didn't come up with the same thing yet, I haven't kept up with most speculation.