#you kill the flayer that tadpoled you it's the one that's stuck in the craaasshhhh

[metaben]

the Flayer at the beginning of BG3 is not the Emperor! Emperor is in the Prism, which SH stole and has in her pack. he only ended up on the ship because SH was kidnapped after stealing the Prism.

Emperor directly explains this to you, but not in so much detail. He was sent by the Absolute to recover the artefact and when he did, he realised he could basically hide inside and use Orpheus' power to interfere with the Absolute and the tadpoles.

SH steals the Prism and gets taken to the ship with the Emperor inside of the Prism. he is never present on the ship. he doesn't leave the Prism until the end of Act 2, briefly as the Guardian

there are a lot of ambiguous parts to his story but how he ended up on the ship and whether or not that Flayer is him, are directly explained to you. they're not intended to be the same Flayer. they intentionally gave them different eye colours to distinguish them

EDIT TO ADD: You find the Flayer who infected you on the beach, pinned beneath debris. the narrator TELLS YOU that's the same Flayer from the beginning. The yellow-eyed Flayer is NOT Emp!