Act 3: Confront the Elder Brain Walkthrough

Baldurs Gate 3 - Confront the Elder Brain

This is a complete walkthrough of the final Act 3 Main Quest, Confront the Elder Brain, in Baldur's Gate 3 (BG3). Read on to see a detailed walkthrough for this Act 3 main quest including important notes for the quest, relevant choices that need to be made along the way, as well as the different endings for BG3!

Confront the Elder Brain Walkthrough

Confront the Elder Brain Objectives

Get Gortash's Netherstone

Baldurs Gate 3 - Gortashs Netherstone

Gortash's Netherstone can be obtained by defeating him inside his office at the upper levels Wyrm's Rock Fortress. Disable his Steel Watch and defeat the Chosen of Bane to get one of the Netherstones needed to dominate the Crown of Karsus.

Get Gortash's Netherstone Walkthrough

Get Orin's Netherstone

Baldurs Gate 3 - Orins Netherstone

Orin's Netherstone can be obtained by defeating her inside the Temple of Bhaal underneath Baldur's Gate. Unravel the plot of her Bhaalist cult and defeat her Slayer Form to get one of the Netherstones needed to dominate the Crown of Karsus.

Get Orin's Netherstone Walkthrough

Head to the Morphic Pool

Once you have all three Netherstones secure, teleport to the Temple of Bhaal Waypoint. From there, head north until you find the Morphic Pool Dock Waypoint and interact with the Skiff to start the Confront the Elder Brain main quest. This is a point of no return. When started, you will no longer be able to revisit the Lower City or your Camp.

After watching the cutscene that takes you across the underground lake, make your way towards the Morphic Pool. Fight your way through packs of Intellect Devourers and Intellect Gluttons until you reach the massive cavern housing the Elder Brain.

Confront the Elder Brain

Baldurs Gate 3 - Confronting the Elder Brain

You will be subjected to 4 Ability Checks once you do come face-to-brain with the Elder Brain. It will not matter if you pass the DC20, DC25, DC30, and DC99 Ability Checks since the Elder Brain will shrug off your attempts to dominate it using the Netherstones.

Once you pass or fail the DC99 Ability Check, the Emperor will appear and drag you back into the Astral Prism. Inside, you will need to devise a new plan to combat the evolved, Netherbrain.

What Do You Get for Passing the DC99 Check?

Passing the DC99 Ability Check during the Morphic Pool sequence affects the final boss fight by inflicting the Against All Odds condition on the Netherbrain (when you finally face it).

Once you successfully dominate the Crown of Karsus and enter the portal to the Netherbrain (during the final boss fight), you will find that its starting HP has been reduced to 240 out of 300. This makes it easier to kill it within 1-2 turns.

What Happens if You Submit to the Elder Brain?

Baldurs Gate 3 - Dominated by the Elder Brain

If you submit to the Elder Brain you will get the Game Over screen. Your characters will transform into Mind Flayers, similar to what happens if you kill the Emperor during the Help Your Protector main quest.

Side with the Emperor or Orpheus

Inside the Astral Prism, the Emperor will tell you that the Netherstones are not enough to dominate the Netherbrain. For the original plan to work, you will need to trust the Netherstones to the Emperor as only a Mind Flayer can dominate the Netherbrain.

Players who obtained the Orphic Hammer will now have to choose between siding with the Emperor or siding with Orpheus. If you do not have the hammer, you will only be able to side with the Emperor.

Note: Choosing either the Emperor or Orpheus will naturally affect Lae'zel's ending. Take note of this especially if you didn't bring her along when confronting the Elder Brain at the Morphic Pool.

What Happens if You Free Orpheus?

If you free Orpheus using the Orphic Hammer, the Emperor will leave the Astral Prism and join the forces of the Netherbrain. During the final battle, he will appear as one of the enemies you have to defeat.

Additionally, by siding with Orpheus, the Emperor will summon your party's Dream Visitors instead of the regular Countermeasure enemies conjured by the Netherbrain, during the final battle.

What Happens if You Assimilate Orpheus while Partied with Lae'zel?

Baldurs Gate 3 - Laezel Leaves the Party

Lae'zel: You want Orpheus dead? You'll have to kill me first (moments before she gets bodied).

If Lae'zel is in your party and you decide to join the Emperor, she will threaten to kill you. Players will be given the option to side with Orpheus, persuade Lae'zel, or attack Lae'zel when this happens.

In order to convince Lae'zel that this is the only way to beat the Netherbrain, you will need to pass a DC30 Persuasion Check (Charisma) in order to keep her allied. Otherwise, she permanently leaves the party and attacks you.

Choose Who Becomes an Illithid

Baldurs Gate 3 - Choose Your Illithid

If you sided with Orpheus, you will need to choose who becomes a Mind Flayer. Only your current character or Orpheus can be chosen to become an Illithid. Naturally, this choice will affect the ending scenes after you beat the Elder Brain.

If you sided with the Emperor, you can still choose to become a Mind Flayer. This choice affects the ending sequence when dominating the brain since you will not need to pass any Ability Checks if you want to unlock the Becoming the Absolute ending.

The Emperor Will Not Have All Illithid Powers

If you do side with the Emperor, do note that he does not have all the Illithid Powers available to him. Unlike Orpheus or yourself (if you decide to become a Mind Flayer), the Emperor will only have a limited selection of powers, making him less effective during battle.

Transforming Into an Illithid Before Freeing Orpheus Unlocks New Dialogue

Baldurs Gate 3 - Orpheus Mentions the Legend of Oryndoll

Orpheus: It is as if I am reliving the legend of Oryndoll. You are the illithid Urengol, rebelling against your own hivemind. And I am the noble githyanki Valraag who must now reconsider his position.

If you ask the Emperor to transform you into an Illithid then choose to free Orpheus afterwards, the Githyanki Prince will be more welcoming. In fact, he will welcome you as a rebel Illithid, proposing an alliance to defeat the Netherbrain.

Battle Through the Upper City

Baldurs Gate 3 - High Hall Courtyard

Once you leave the Astral Prism, your party will arrive at the ruined Upper City of Baldur's Gate. Meet your allies during the opening sequence, before fighting your way through the High Hall Courtyard in order to reach the Netherbrain.

There will be a lot of enemies during this fight including Mind Flayers, Intellect Devourers, an Ogre, a Spectator, Absolute Cultists, and Goblins. Make sure that you use the Call Forth Allies feature and summon help to make this enemy-dense area easier to complete.

Pass Two DC20 Ability Checks to Secure the Help of the City Watch

Baldurs Gate 3 - City Watch Allies at the High Hall Courtyard

When you first approach the High Hall Courtyard, a group of City Watch soldiers will be seen fleeing from the Mind Flayer invaders. During your dialogue with them, you will need to pass a DC20 Insight Check as well as a DC20 Ability Check to secure their help for the upcoming fight.

Reach the Netherbrain's Stem

Baldurs Gate 3 - High Hall

Inside the High Hall, your only objective is to reach the set of Double Doors leading to the Brain Stem at the top of the crumbling structure. Avoid combat during this segment since the Nautiloid will continuously rain down cannon fire and send enemy reinforcements during your trek up.

Tip: If you or Orpheus chose to become Mind Flayers, this part will be easy since your modified Fly ability will use up 4m of movement instead of just movement. This allows you to use Fly twice in a single turn, making it easier to reach the double doors within 2-3 turns.

Use the Restoration Pods to Fully Replenish Your Party's HP, Spell Slots, and Actions

Baldurs Gate 3 - Restoration Pods

The two Restoration pods available in the Upper City will fully replenish your Party's HP, Spell Slots, and Actions. They will function like Long Rests since you will not be able to return to camp at any point once you start the Confront the Elder Brain main quest.

Defeat the Netherbrain

Baldurs Gate 3 - Confronting the Netherbrain

Once you reach the top of the brain stem, the final battle will begin. This will be a battle in two phases. First, you will need to dominate the Crown of Karsus using the Netherstones. Next, you will need to enter the portal and defeat the Unbreakable Will of the Netherbrain.

During the first phase, escort your Illithid companion to the Crown at the far end of the arena. Have them cast Karsus' Compulsion until the next turn to open the portal to the Netherbrain. If they get interrupted or downed while casting, you will have to repeat the process all over again.

Inside the portal, use everything you have to defeat the Netherbrain. Summoned allies will not be able to follow you inside. Only your Illithid companion along with your 4 party members are allowed to confront the Unbreakable Will of the Netherbrain.

Dominate the Netherbrain

Baldurs Gate 3 - Dominating the Netherbrain

On defeat, a cutscene will trigger. You will have two options when choosing to dominate the brain: allow it to destroy the tadpoles then itself or dominate the brain and become the true Absolute.

The first option will unlock the ending cutscene that shows the companion quest conclusions for each of your party members. The second option will unlock the Absolute ending that has you become the leader of the Grand Design.

If you sided with the Emperor, you will get an additional option to rule as the Absolute together. However, be warned as it will be the Emperor who leads instead of a joint partnership based on the cutscene that plays afterward.

What Happens if You Choose to Betray Your Allies?

Baldurs Gate 3 - Betraying Your Allies

Unless you chose to become the Illithid that controls the Netherstones, betraying your allies will require you to pass a DC12 Strength Check to succeed. If you manage to pass it, you pull out a dagger and murder the Emperor or Orpheus during the final scene.

Once you take control of the Netherstones and dominate the Netherbrain, you unlock a unique ending where your character becomes the Absolute, bending the world to their will. This grants you the Absolute Power Corrupts achievement.

All Endings in Baldur's Gate 3 (BG3)

Notification IconNotice from XGamer These are the general endings you can get based on the decisions made while dominating the Netherbrain. This list will not include the individual companion endings after you get rid of the tadpoles.

Destroy the Tadpoles and the Netherbrain

Baldurs Gate 3 - Destroy the Elder Brain Ending

Players who want to find out what happens to their companions after destroying the Absolute should choose this ending. After defeating the Netherbrain, choose the option to command the brain to destroy all the tadpoles and then itself to unlock the ending.

Once the brain crashes into the bay, you will be treated to multiple cutscenes that showcase the ending scenarios for each of your companions. Choosing this ending will unlock the Hero of the Forgotten Realms achievement.

Dominate the Netherbrain and Become the Absolute

Baldurs Gate 3 - You Become the Absolute Ending

Another ending would be to dominate the Netherbrain and become the Absolute. If you did not choose to transform into a Mind Flayer, you will need to pass a DC12 Strength Check to betray your companions and become the Absolute. Getting this ending unlocks the Absolute Power Corrupts achievement.

Convince the Emperor to Join You as the Absolute

Baldurs Gate 3 - Emperor Becomes the Absolute Ending

There is a third alternate ending if you sided with the Emperor and gave him control of the Netherstones. Convince him to join you and become the Absolute to get a variation of the evil ending. Instead of you taking the throne of the Absolute, it will be the Emperor as shown during the cutscene. This ending also unlocks the Absolute Power Corrupts achievement.

Baldur's Gate 3 (BG3) Related Guides


Main Campaign Walkthrough

Act 1 Campaign Walkthrough

All Act 1 Main Quests
Prologue Find a Cure

Act 2 Campaign Walkthrough

All Act 2 Main Quests
Infiltrate Moonrise Towers Help Your Protector

Act 3 Campaign Walkthrough

All Act 3 Main Quests
Get Gortash's Netherstone Get Orin's Netherstone Confront the Elder Brain