Butt-kicking for Goodness!

'Current incarnation' is important here. The opening cinematic has existed since early access, which means it has existed since before the Emperor was probably a character. It was rendered back when the dream visitor was still Daisy; a manifestation of the tadpole.

I ultimately don't think it matters if that Illithid was always meant to be the Emperor or not. What matters is the current narrative, and within that context I do think they are meant to be one-in-the-same.

Hear me out.

We know the Emperor was assigned as the captain/pilot of the Nautiloid sent to steal the Astral Prism. We know there are dead Illithids littering the spelljammer before the ship reaches Avernus. We know the body of the strike-force captain is never recovered from the crash site. Importantly, we know this is a strike-force ship with a specific purpose. There's no reason for the Elderbrain enthralled Illithids on this mission to deviate away from returning to Moonrise Towers once the Prism is in their possession, and whilst it could be argued that the intention was to lose their Githyanki pursuers-- openly attacking the city of Yatar is just such a strange move. There's no real reason for it. This isn't an abduction mission to find more hosts (in fact, that's not even how the Chosen Three are infecting people to begin with), and an outright attack on a city at this point in time runs counter to the Chosen Three's plans of careful subterfuge. Besides, Gortash would have certainly documented it (as he does everything else regarding his schemes).

However, if we operate under the idea that the Emperor is the cinematic Illithid, certain things tend to make more sense.

The Emperor is fleeing for his life from both the Githyanki and the Elderbrain while trying to formulate a plan on the (literal) fly. He needs allies, so he decides to make some. The best outcome he can hope for is that he snatches someone up with as strong a sense of self-preservation as him (and does he ever. It's us). Additionally, a Nautiloid attack is big news which would suddenly put Mind Flayers at the forefront of everyone's thoughts.

The last we see of the cinematic Illthid is it reeling from an explosion due to dragon's fire, at which point there is a break in time and the tutorial starts. This would give the Emperor time to retreat into the Astral Prism to begin his recovery/battle with Orpheus' honour guard. Based on how we find Shadowheart -- awake and aware and with her pod surrounded by a swirling, orange-red ribbon of magic (that is repeatedly used later in the game to depict Orpheus' psionic power) -- I believe the Emperor is in the Prism at this point doing shit. Now, I know that in Act 1 there are two instances of the narrator talking about the Illthid that infected the player. The first is the dying Illthid at the crash site, of which the narrator describes as "the thing which abducted you". The narrator is talking about the species of Illthids as a whole in this moment. One look at the dying Illithid makes it clear it is not the one that personally infected you as it has completely different clothing.

As a brief side note, I want to point that the Emperor is not the only Illithid in the game with that ornate outfit. There are Illithid corpses at the crash in the same attire.

The second instance is a little more interesting: the dead Illithid at the Goblin Camp. One of two things can happen there and I have now experienced both. Either the narrator will tell you "this is the Illithid that infected you", or "this is not the Illthid that tormented you. Its build is smaller. Its clothing less ornate." The thing is, I am pretty sure the model is different between these two scenarios. I distinctly recall the ornate clothing on the body during my first playthrough when the narrator confirmed it as the one which tadpole'd me. On my second playthrough the corpse was indeed one with less fancy armour. For context, I started my first playthrough in Sept. 2023 and the save file survived all of the major updates (though was a bit buggy near the end). I have no idea if I am either misremembering things, if there is a trigger which determines which corpse you get, or if Larian quietly patched it in one of their updates for continuity purposes.

In addition to all of this, there's a dialogue in Act 3 with Raphael which I always found interesting. When offering his deal, you can tell the devil that the Emperor is the only reason you're still alive, to which Raphael will respond with, "On the contrary, it's the reason you're in this mess." While Raphael is an untrustworthy liar, this comeback only makes sense if the Emperor was the one that abducted and infected you. Or perhaps Raphael is simply trying to make you think that so you turn against your squid buddy and sign the contract. There's also the matter of the tadpole the Emperor offers the player at the end of the game which will complete the ceremorphosis process. He states he took it from the Nautiloid and has been nurturing it ever since specifically for your use. I presume in this instance the 'you' was originally a general 'whoever survives/is the strongest', only to eventually become specifically for the player once he grows attached. Do note though that he only ever offers this to you if you ask him.

Personally, I like the idea of the Emperor being the cinematic Illthid. Balduran was one of Faerun's most famous pirates adventurers and ship captains. That Illithid is doing some fancy flying. The idea that he abducts and infects the player* doesn't change my opinion on him at all. Much like the companion arc of a certain vampire spawn, the Emperor also begins our relationship with him viewing us as a means to an end (his freedom), only to accidentally catch feelings because we treat him as a person.

Well, some of us at least. *I know different origins are infected differently (Wyll, Karlach, Durge). Astarion and Tav are curiosities, being Baldurians aboard the Nautiloid before the attack on Yatar. Since that Nautiloid never attacks Baldur's Gate, that means Astarion and Tav would have to end up on the Nautiloid in a similar manner as Durge. Astarion states he was in the city when abducted by beasts. The only explanation I have for this is that Astarion and Tav were abducted for infection to be used as fodder in the strike-force mission. Technically, that means if the Emperor is the cinematic Illthid, he only abducts and infects the player if you're playing as Shadowheart or Lae'zel. ;)

Anyways.