Choosing your path is essentially the last choice you'll make in G3. First of all, you have to find Xardas and all of the Adanos' artifacts, then A) destroy them / give them to I) Rhobar / B) Zuben and then A) kill both Rhobar and Zuben / I) liberate Myrtana / B) kill everyone. :P
Also, a chaos outbreak may happen once you choose a god, for example hashishins attacking orcs (and vice versa) in Montera, Cape Dun, Trelis, Geldern and everywhere else.
If you want it the quick way, though, just get all five artifacts and bring them to Rhobar. He'll give you the Scepter of Varant, which you can use to communicate with Innos through his statue in the Monastery.