Nzoth was definitely still imprisoned at the time so it wasn't him shapeshifted.
Hell he more than likely still is right now.
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Much less so many things that the devs say are incredibly wrong and off that even if they did say it I don't trust off the cuff comments from devs as being canon at this point.
Azeroth "forces" not a threat for Old Gods, because we cant kill them fully. He needed us to face Legion and Sargeras! Imagine "end times" happend and like 5-10 yrs later Sargeras rides in Azeroth on his BigD Sword with whole Pantheon corrupted. That a real DEAD END for Old Gods and not only on Azeroth!
Easy, they could always say that N'Zoth's Void overlords were forcing him to go through with the Hour of Twilight but he had different plans so he created an avatar for himself (Wrathion) that the Void would have no control over and then stopped the Hour of Twilight. That's why the Void showed Alleria visions of herself killing N'Zoth and taking his place. There's also this:
After being absent in the expansion that he directly caused, the only thing that could redeem Wrathion as a character is if he turned out to be N'Zoth.Wrathion says: Do you deny it? The dark visions? The voices in your head?
Fahrad says: No. No! I'm in control of the voices. They're there to help me.
Wrathion says: And what are they telling you now, Fahrad? What do your dark masters whisper?
Fahrad yells: Kill.... they want me to kill you now... oh, why did you have to go and anger them?
Fahrad yells: You have proven too difficult to control!
The old gods do not want to annihilate life though, they want to enslave it, or otherwise they'll never be able to corrupt the titan since they need their slaves to free them beforehand since they can't really do it from their current and shackled position (or not to the amount they need to corrupt her).
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As seen with Y'shaarj, cutting him apart didn't really kill him, the corruption and his essence still resided within the imprisoned heart.
Think Y'shaarj is the only old god that's actually dead, doubt C'thun / Yogg'saron are even close to being dead.
Silas Darkmoon is N'zoth.
Xal'Atath describes them as being defeated as much as Y'Shaarj was. I also think that the Sha-like remnants we saw in Ulduar before Legion don't necessarily make Yogg alive. They're echoes, not Yogg itself. C'Thun's remnants whisper in the Med'an comic to have Cho'Gall resurrect him-you don't resurrect something that isn't dead.
The analogy I saw around that I like was that the Titans removing Y'Shaarj was like tearing a parasite out of flesh. It's going to do more damage, but a smaller, more surgical procedure could kill them effectively.
We do need some clarification on how dead the Old Gods we've fought are though, hopefully BfA will bring some much-needed clarity. There's a lot of conflicting and dated Old God lore that could do with clearing up.
He could only be destroyed fully by an artifact that could only harm Dragons in a major way. The only way we got said artifact was abusing the timeways. Nozdormu broke his duty of maintaining the timelines so we could defeat Deathwing. And even though Deathwing died, the other aspects lost their power for good and their flights can no longer breed.
Considering that Deathwing never put his power into the Dragon Soul, it is possible that the Earth-warder's powers can be passed down to another, similar to what happened with Kalecgos. It is also possible that black dragons can still breed, providing there is any brood mothers left.
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The AvH war was already underway by the time he got involved in it during patch 5.1. He wanted the war to end quickly, he originally thought the horde would win since they would do anything to win. Even if that meant using the Sha, which is something Wrathion was fine with since he empowered us with a few sha touched gems. However after Vol'jin began his rebellion, Wrathion sided with the alliance, hoping that Varian would integrate the horde rebellion into the Alliance. However that never happened. Also he did actually care with side won. He threw a massive tantrum when he heard that the "idiot King" allowed the horde to exist as a separate entity.
I've always wondered about ill'gynoth's "your coming was foretold in the rings" quote, and the fact that Wrathion in whelp form is watching us get our legendary rings in Draenor.