If you remember the dialogue with him then you shall see that he has great wisdom and simply waits for events to pass by and futuer to unfold.
You are, however, mistaken: he does not travel through time, he travels along the same time-frame as everyone else. What he has is the temporal version of the Sight: he is able to see the most likely paths the future will take, the past and the present. He percieves beyond and above linear time, but he does inhabit linear time.
What he does with the Main in the pit is best verified by Craig himself, but it is likely, from the dialogue, that he simply allows the Main to share his (Malignus') vision of the past and the futures which concerns the Main.
The only discord are the Dean and Nelis battles, but that's maybe simply due to taking short-cuts with coding and not allowing the player to return to the main game.