I like think of this :

Long before the Emperor attained Godhood he meet the Doomslayer (Mind you the Doomslayer can travel through universes) and was inspired by him. And found him a perfect example of a human being and a good person be that a violent one. (And I like to think he based his sons and his Primearchs off of the Doomslayer) And Doomslayer like the Emperor too . Seeing him as a younger him . We now fast forward to the current timeline in the Warhammer 40K Universe. The Emperor Is growing displeased with they way humanity is now . And when he reaches his breaking point he uses his powers to call out to the Doomslayer to aid him in his plans to reform the Imperium and finally taking down the demon lords of chaos (And kind of the reason the Doomslayer would be there in the first place) With the Doomslayer acting as a representative and the the muscle of the Emperor till he can finally regain his human form .