The end of Act 2 of Baldur's Gate 3 shows the true evil pulling the strings behind the scenes that orchestrated the events of the game so far. Now knowing who your true enemy is, you and your party venture off to Baldur's Gate to prepare both yourself and the city for the coming attack.
On your way to the city, you'll be attacked by a group of Gith that want you dead because of the Tadpole in your head. After running through a portal to the Astral Plane, you'll meet a Mind Flayer known as the Emperor, who will request your help in stopping the Gith assault.
Should You Help The Emperor
Despite the Emperor being a Mind Flayer, they are who you need to side with in this fight. The Emperor will also be able to prove himself to be the Dream Visitor who has been helping you up until this point and will be able to explain things further after you help them take out the Gith.
Siding with The Emperor will have you fight alongside them against the invading Gith. The following battle can be a little challenging depending on your level, as the Gith monks will have many attacks each. The Emperor will use their abilities to fight alongside you and will prove themselves as a useful ally. After the Gith have been defeated, you can ask the Mind Flayer different questions to get the full scope of what happened at the end of the last Act.
Killing The Emperor
While the Gith won't ally themselves with you, a Mind Flayer is a Mind Flayer. While The Emperor is different, you can choose to attack and try to kill the Emperor during this encounter. Should you kill the Emperor, you'll quickly see they were the one trying to protect you. Without the Emperor imprisoning the powerful Gith, they will escape, and you'll lose control to the Tadpole in your head, be found by the Absolute, and turn into a Mind Flayer, ending your story. There is no way to avoid this fate if the Emperor dies, so protecting them is a must in this situation.