There are two theories right now :
1 - Flemeth/Mythal took control of his body
Evidences :
-Flemeth takes control of willing living bodies to extend her existence. Solas says he is willing to pay the price for having broken the orb, that may be the price he's reffering to
-Flemeth was gathering god souls already, like how she took Kieran's Old God soul in the Fade.
-Mythal is looking for revenge for having been reduced to a wisp that is forced to hang onto Flemeth to survive, and Dread Wolf is apparently the one who betrayed the rest of the Elven gods. But if that's who she wanted to take revenge from... That revenge is done, what is left for her to do ?
-Mythal is one of the two leaders of the Elven pantheon. She outranks Dread Wolf so it'd make sense for him to savrifice himself to her.
2 - Solas/Fen'Harel/Dread Wolf took Flemeth's two god souls
Evidences :
-The Dread Wolf is the Dragon Age equivalent of Loki, he's a treacherous one. He's the one that has supposedly destroyed the rest of the Elven pantheon and locked away the Forgotten Ones.
-A spirit/soul like Mythal/Cole can't force itself onto an unwilling body, but never did they say it would be impossible to steal the soul of someone who would very much want to keep it. In fact Mythal takes control of whoever drank from the well of sorrow so yeah, those guys are indeed able to force their will sometimes, possessing a body is the exception but not the rule of thumb.
-He said to the inquisitor "whatever comes next, know that I'll always respect you", implying what he's going to do next is probably not going to please the inquisitor. Although it could just mean he's not showing up ever again.
I'd favor the first theory, Solas has been a good, helpful pal since the beginning and I'd doubt even the Dread Wolf could lie to us that well. Mythal has a motive, but she's not really aiming at mortals, she says she'll shake the heavens. But who is there to shake ?
-The gods of the old elves ? Mythal and Fen'Harel are now confirmed, but we've yet to see the Forgotten Ones, or the rest of the Elven pantheon. Flemeth has been betrayed by her husband and that's the reason Mythal empathised with her. Thing is, Mythal's husband is the second leader of the Elven pantheon, so that is plausible that he is her target, and it's not unheard of him to go mad.
-The Old Gods of Tevinter ? They're the ones that transform into Archdemons and cause the blights, so yeah, they're pretty concrete as well. There were 7 of them, 4 are dead, 2 are still asleep, and 1 is in Mythal/Fen'Haren's possession now. Tevinter and the Old Elves were at war so it would make sense for their respective pantheons to be at war too. Actually, the Old Gods were dragons, and Flemeth can turn into one as well. The Elven Gods were at war with similar beings, called the Forgotten Ones, it would be possible that the Old Gods were in fact the Forgotten Ones. After all, this franchise is named Dragon Age.
-The maker ? He is very much absent, but his city can be seen in the fade by every mage in Thedas each night, when they dream. But the Maker may be an invention to try to explain the existence of the Black City rather than an actual deity. In that case, who does the city belong to ? It must not be here by chance, and the blights started when mortals like Corypheus decided to go there, so it is definitely extremely important to this whole thing.
-The dwarves and the Qunari aren't really religious. The dwarves pay hommage to their ancestors, Mulan style, the Qunari follow a philosophy rather than a religion.
Whoever it is and whatever their plan is, the next game's villain is now in possession of three gods' souls : Mythal's, Fen'Haren's, and Urthemiel's, and is at least three times as powerful as anything else we've ever seen in the Dragon Age franchise. I'm pretty hyped about this =P
The pieces of the puzzle are coming along nicely, I'm pleased !