Board Thread:Lore Discussion/@comment-9062114-20141010174543/@comment-24349111-20141011091012

It is heavily hinted at that the Thalmor were responsible for the Void Nights. MK outright says that the Void Nights were a eugenics experiment by the Thalmor, obviously to test what would happen to Khajiit born without the moons.

They were also responsible for preventing the Daedra in the Oblivion Crisis to completely flood the Summerset Isles, similar to how the An-Xileel managed to fend the Daedra off.