Captured By Mind Flayers - Baldur's Gate 2 Side Quest
The Captured by Mind Flayers side quest begins when you enter the Underdark Eastern Tunnels and take a few steps forward. A group of Mind Flayers will appear to capture your group and will immediately put you into jail. You will be approached by an Ogre and told about your predicament, essentially you have to fight in an arena for the Mind Flayer's entertainment.
Your first battle will be against a group of Umber Hulks; when it is over you'll be returned to your cell at which point you'll want to enter the adjacent cell and speak with Simyaz, the Githyanki's leader. Simyaz and their group will be teleported away to fight but when they return they'll tell you their plan. The Githyanki will distract the Mind Flayers with their own spells during your match while you break out of the prison and cause havoc.
During the match you have with the Githyanki they will uphold their end of the bargain and will use their spells to attack the Mind Flayers. Help them by defeating the Kuo-toan enemies then open the door on the eastern side of the arena with your Thief. This will give you access to the prison area and by extension the main compound.
Below I have provided a step by step list of how to escape the Mind Flayer city. If you need additional help finding some of the locations I talk about then use the pictures below.
How to Escape the Mind Flayer City:
1. Visit the Illithid Serum Room in the eastern portion of the map; collect Illithid Serum
2. Use the Illithid Serum on the machine next to the slaves in the room to the south
3. Obtain 2 - 4 Control Circlets from the machine in the room with the slaves
4. Use a Control Circlet on one of the Mind Flayers that spawns in the Illithid Serum Room
5. Bring the mind controlled Mind Flayer to the locked door and click on the door while controlling them to open it
6. Visit the Master Brain in the northwestern corner of the map and defeat it
In the Illithid Serum room you'll find a single Mind Flayer who will respawn once every couple of minutes (this is important) along with big red vats. Mouse over the big red vat and you'll notice that you can click on it; a picture of what I am talking about is shown below. Click it a few times until you receive the Illithid Serum. Once you have this item you'll want to go into the room marked Slave Room on my map above. It's the room just south of where we got the serum.
What we have to do in the Slave Room is use the Illithid Serum we just got on the weird looking machine next to the slaves. There are a couple of these machines and it doesn't matter which one you use it on. A picture of the machine I am talking about is shown below.
Adding the Illithid Serum to this machine will cause the slaves to awaken and speak with you. The slaves will inform you about the ability to make Control Circlets using the other larger machine in this room. You can make a total of 4 Control Circlets and I strongly recommend you do so as we're going to need these to open doors throughout the city.
Illithid Serum Vat
So, in order to proceed to the rest of the Mind Flayer city you're going to have to open the locked doors. When you click on the locked doors throughout this compound you'll get the message, "Only a powerful mind or godly strength will force this door open". This gives us 2 ways of opening these doors, the first of which is to mind control a Mind Flayer and use them to open the door. You can do this with a Control Circlet that you make via the machine shown above. Any of the Mind Control spells will work too if you run out of Control Circlets.
Alternatively, if you're playing an evil character in an evil party you can use your Slayer Form ability to break down the door that way. Keep in mind that any time you use Slayer Form you'll lose 2 Reputation and there is a chance that good companions in your party will abandon you. For this reason, you'll probably want to use the Mind Flayer to open the door instead.
Once you bring the Mind Flayer close enough to the door it'll automatically open up and the Mind Flayer will attack you.
Upon opening up the first set of locked doors the group of Githyanki will teleport in and speak with you. They basically tell you that you need to kill the Master Brain to leave this dungeon and they wish you luck before teleporting out. You can find the Master Brain in the northwestern most portion of this map and in order to reach him you'll have to Mind Control a few more Mind Flayers to open some doors.
Tip: If you are having trouble defeating these Mind Flayers I strongly recommend you check out my Baldur's Gate 2 Beginner's Guide. That guide will provide you with strategies for Mind Flayers as well as strategies to help you get better at the game and better at the different classes within the game.
As you may already expect the Master Brain is going to be a tough fight. In the room with it are 2 Ulitharid enemies as well as an Umber Hulk; I recommend you take out these enemies first then focus entirely on the brain.
During your fight with the Master Brain it can create 'Brain Golem' enemies which are essentially Clay Golems that can only be damaged with magical weapons that deal crushing damage. Focus on the Master Brain and ignore these golems until after the fight. Once the Master Brain dies the front door leading back to the Underdark will open and you'll officially be done with this dungeon!
To complete this side quest you'll have to head back out to the Underdark and speak with the Githyanki's that we escaped with. You can find them in a small camp just across the chasm heading east away from the Mind Flayer city. This interaction will end in bloodshed unless you hand over the silver blade they want, either way talking to them completes this quest.