Board Thread:Warhammer 40k General Discussion/@comment-14745711-20140928092626/@comment-3416287-20140930085256

If any of the primarchs returned, there would be a schism the likes of which hasn't been seen since the Age of Apostasy or the Horus Heresy. The Inquisition would declare the primarch(s) as heretics or daemon puppets.

On the side of the primarch(s):

Most, if not all of the space marine chapters.

The Custodes.

All the astartes of the Deathwatch.

Maybe some elements of the Ecclesiarchy.

Maybe some elements of the Mechanicus.

Maybe the Grey Knights.

On the side of the Inquisition:

Imperial Guard.

Most, if not all of the Ecclesiarchy.

The highlords of terra(maybe with the exception of the Mechanicus).

Maybe some elements of the Mechanicus.

Maybe the Grey Knights.

The Assasinorum.

I think that the Mechanicus would likely sit on the fence, they would help whichever side they think would benefit them the most.

As for the Grey Knights, they might just refuse to participate, or they would venture outside the Imperium to kill daemons until the conflict was over, because they are loyal to the Inquisition, but they may also feel honourbound to serve the primarchs.