Board Thread:Warhammer 40k General Discussion/@comment-25618639-20150426193759/@comment-25177957-20150502102146

There was no way the Emperor was in any position at the time to fight the Mechanicum, he needed starships and supplies, and the majority of resources on Terra were exausted and there was little industry left. The Emperor went as far as to tolerate the Mechanicum's religious beliefs for essentials.