Board Thread:Lore Discussion/@comment-7185849-20130318192711/@comment-6707115-20130618183726

The lore is very vague about what happend to Vivec seeing as how killing him was a possiblity because Azura told the Nerevarine to do it, though unlike Almalexia and Sotha Sil his elimination quest has the possiblity of leaving him alive. So that's why there are three threories: snatched away by Daedric Princes, retired from public life to meditate on his philosophy somewhere in Morrowind, or just straight up killed by the Nerevarine.