Originally Posted by Zerubbabel

The Artifact timeline is pretty broken still. It is not clear how it goes from Vlaakith to Emperor to Shadowheart to Emperor to Shadowheart. Clearly the following needs to happen:
1. Emperor steals it from Vlaakith.
2. Shadowheart steals it from Emperor.
3. Emperor steals it from Shadowheart and finds a way inside.
4. Shadowheart somehow gets it back while Emperor is inside and Shadowheart is imprisoned.

Alternatively, the Emperor is the Mindflayer with which the PC locks eyes before being taken out by a brick. Which makes the timeline:
1. Emperor steal Artifact from Vlaakith, is freed but hides this fact as the party can to other True Souls.
2. Emperor tadpoles everyone and plants Artifact on Shadowheart Whom he caught trying to steal it.
3. While the Nautiloid is crashing, Emperor goes into the Artifact and saves everyone.

Originally Posted by Cawyden

3. That is the thing - we don't know for 100%. We know the Emperor was on the ship (among other mindflayers, intellect devourers and a tadpoled strike team) but the one in the cinematic does NOT look 100% the same what you noticed too. And we don't have any reaction from Tav/companions/Emperor that he is the one who tadpoled them, which is very strange. Why didn't make Larian make the Emperor model look the same and add at least one dialog line about him being the one that tadpoled Tav/companions? So - yes it is very likely that he is the one but it isn't so clear as you wrote it.

Sorry, but for 4-5 you weren't certain but the brain says it was his action to free the Emperor so we know this for sure and don't need to assume things. And he says he broke free the moment he found the astral prism and not sometime later. Meaning he very likely was already free at the time of the cinematic. Maybe already in the prism, if he wasn't the mindflayer in the cinematic.

So, I fired up a new game to check out tentacle bro you share eye contact with before getting yeeted off the ship.

[Linked Image from cdn.discordapp.com]
Cawyden is correct in that the eyes of Emperor are purple, while the one in the cinematic, and this fella over here, are orange. And based on the fact that the Mind Flayer on this screenshot also has wildly different clothing compared to Emperor, I doubt Emperor had dressing in his priorities at that time, even with the inconsistency of the plot.

Honestly though? I am still willing to accept that the Mind Flayer in the cinematic IS Emperor, mainly based on the fact that Larian forgot about the fact that Emperor is quite literally Balduran, and so has Emperor by proxy - but of course, the facts don't suggest so. Therefore, we can assume that Zerubbabel's first timeline is what is correct.