Confront the Elder Brain - Baldur's Gate III Guide - IGN (2024)

Have you got Orin's Netherstone and Gortash's Netherstone in your inventory? If so, it's time to prepare for the final section of Baldur's Gate 3 and head to the Morphic Pool in order to confront the Elder Brain. Here, you'll get to wrap up the game and experience one of multiple endings, depending on your choices.

This is one of the most interesting parts of Act 3, especially thanks to the addition of the Gather Your Allies quest. Your experience here will really depend on the choices that you've made, and it's worth playing through the final Act multiple times in order to experience all the possible outcomes.

Below, you'll find a complete Walkthrough for the Confront the Elder Brain quest, including key item locations, fight techniques, and important lore snippets.

Confront the Elder Brain BG3 Walkthrough

This is a long final quest. Use the links below to navigate through the Walkthrough where needed.

• Preparing to Confront the Elder Brain
• Getting to the Elder Brain
• Confronting the Elder Brain
• Setting Up Your Attack
• The Battle for the Brain
• Netherbrain Boss Fight

If you're starting from the beginning and don't have a particular section of the quest you need a hand with, keep on reading below.

Preparing to Confront the Elder Brain

Once you've taken down Orin, it's time to track down the Elder Brain and finish this once and for all. Head out of the Temple of Bhaal the way you came, making sure to speak to Yenna/your kidnapped companion as you leave if you managed to save them in time.

As you walk out of the Temple, you will hear the Elder Brain breaking free.

Keep heading out until you are back in the Undercity Ruins. You can head to camp and rest up to recover spell slots if needed. You could even take some time to finish more Side Quests to level up if needed or grab some more items.

Follow the quest marker north to track down the Elder Brain.

As you continue into the depths of the Undercity Ruins, you will notice that there are Cranium Rats swarming near the water.

This means you're on the right track. You'll unlock the Morphic Pool Dock Waypoint here.

Get into the skiff (the wooden boat) when you're ready to head off.

The game will warn you that there's no turning back, then a cutscene will play showing your party sailing into the darkness.

Getting to the Elder Brain

When you come ashore, your party will immediately feel the immense impact of the unbroken Elder Brain.

As you travel forwards (the path is fairly linear, you'll need to jump over a few ledges but there's no way to really get lost) your party will occasionally become Mindbroken, meaning they cannot use reactions thanks to the Elder Brain's influence.

There's a lot of great loot on the way to this encounter. Do take the time to check boxes and chests as you go, you can find some Superior Healing Potions, plenty of gold, and even special kinds of Arrows.

As you get closer to the Elder Brain, you'll end up in a battle with a large group of Intellect Devourers and Intellect Gluttons.

The Intellect Gluttons explode when they die, sending out a caustic liquid. More Intellect Devourers will spawn in during the battle, too. AOE spells are the answer to not getting overwhelmed by the number of enemies here. They don't hit immensely hard, but there are a lot of enemies to contend with.

Once you've defeated the group, you'll notice that the Intellect Devourers and Gluttons were not themselves. They have been corrupted by the Elder Brain.

Heal up, then press onwards to the north.

Jump over the gaps in the wooden bridge, then continue.

There's a locked door near here, which leads to a room with a chest and a dead body. It's worth getting in here as you can get some powerful potions, like a Potion of Angelic Reprieve, and some other handy items like Healing Potions.

You'll enter a clearing here, leading to the Elder Brain encounter. Make sure you're ready to go, save, then head onwards.

Confronting the Elder Brain

As your characters get close to the water, they'll be stunned, then a cutscene will play. Eerie silence will fill the air, while The Emperor encourages you to be ready.

The Elder Brain will then rise out of the water.

What follows is a series of difficult checks as you attempt to confront and control the Elder Brain with the Netherstones. If you want to see the outcome of these checks, take a look in the spoiler tag below, or continue onwards and chance it.

The checks will become increasingly more and more difficult, and eventually, it will become impossible for you to pass them. Something is clearly wrong.

If you choose the 'submit to the Elder Brain' option at any time, the game will end.

This is technically one of the multiple ending options, and it's certainly not one of the best options, but it's worth doing if you're trying to see every possible outcome - and if you have a recent quick-save to go back to.

The Elder Brain will explain how it has been manipulating you this entire time. It's been using you and The Emperor as pawns, getting you to remove the Netherstones from Ketheric, Orin, and Gortash in order to free it.

Then, it will attack you, but The Emperor will come to your aid just in time, pulling you out to the Astral Realm. The Emperor will note how the Elder Brain has evolved into a Netherbrain and that it cannot be dominated by the Netherstones any more.

Follow The Emperor into the skull to continue.

Setting Up Your Attack

You'll need to speak to The Emperor to figure out what to do next.

The Emperor will be observing Orpheus as you approach.

They will note how the issue was not the Netherstones- it was you. The Netherbrain can think three steps ahead of a regular brain, and regular mortals cannot possibly out-think it.

The Emperor believes they can, though. They'll ask you to give them the Netherstones, so that they can 'assimilate' Orpheus and leave the Prism in order to take down the Netherbrain.

You're going to need to make a crucial decision here, and your options will be limited by the choices you've made earlier on in the game.

If you obtained the Orphic Hammer earlier on in the game, you will be able to choose whether you want to side with Orpheus or with The Emperor. If Lae'zel is in your party, she will play an important part here as well.

The story paths that you will need to choose between are as follows:

• Siding with Orpheus. You can only do this if you have the Orphic Hammer. Siding with Orpheus will mean that The Emperor leaves you and joins the Netherbrain, making up part of the Netherbrain's army and turning random enemies into your party's Dream Visitors during the final battle. You'll need to choose whether your main character or Orpheus turns into a Mind Flayer.

If you want to be a Mind Flayer and side with Orpheus, you can ask The Emperor to turn you and then side with Orpheus. This will make him much more receptive to the idea of being your ally.

• Siding with The Emperor. If you didn't pick up the Orphic Hammer, this is your only choice. The Emperor will join you in battle, although it's worth noting they won't have access to all the Mind Flayer abilities unlike Orpheus. You can also still choose to be a Mind Flayer and gain access to all the abilities. This will heavily impact the ending.
• Siding with The Emperor while Lae'zel is in your party. Choosing Orpheus while you have Lae'zel in your party is a big issue. You'll need to pass a Charisma check of 30 in order to convince her to stay. If you fail this, she will leave you and instantly attack you.

For now, we're going to go with the option of siding with The Emperor and not taking the offer of becoming a Mind Flayer.

Once the assimilation has occurred, it's time to get going.

Before you step through the nearby portal, check for any loot. Orpheus drops a very powerful Confusion ring, some gold, and some Healing Potions.

Step through the portal to High Hall. It's time to finish the final battle.

The Battle for the Brain

As you come out of the portal, you'll be in the Upper City. This is where the final boss battle of Baldur's Gate 3 will take place, and right now, it's absolute chaos. Nautiloid ships are swarming the city and everything appears to be on fire.

The quest marker is pointing east, towards the Netherbrain.

As your party will note, it would be possible to use stealth to get through the chaos, but it's much more realistic (unless you have lots of stealthy characters) to fight your way through.

It's important to note that you won't be able to go to camp or take a Long Rest anymore. There is a Restoration Pod up ahead, but you're going to need to play it safe with spell slots and health. Don't burn through all your potions and scrolls right now.

Head up the stairs and into the building ahead.

Here, you'll get to meet your allies. This is where the Gather Your Allies sub-quest comes into play. If you saved someone or helped them fulfil their purpose during your run, they'll be here ready to support you during battle. As we said back in Act One, this is a game that really values player choices.

As you approach, Beorn Wunterbrood will be giving a speech.

If you're with The Emperor, he will be suspicious of the Mind Flayer, but Withers will vouch for you and The Emperor, too.

Whoever your allies end up being (in our first playthrough, we had Beorn and his troops, Jaheira, Valeria, and Volo), you will be able to summon them during the final battle with the Call Forth Allies ability.

Some allies will also offer passive boosts.

For example, Volo will give your entire party a buff that gives them +2 to their attack rolls, ability checks, and saving throws.

Before you charge off into battle, take full advantage of the fact that there's a vendor here who has lots of useful items. He can be found at the bar and he's incredibly excited to be there.

When you're ready to go, save your game then head out and start heading up the stairs to the north of the building.

As you reach the top of the stairs, you'll encounter a group of fleeing Watchmen. They're frightened of The Emperor, and you'll need to roll well in order to convince them to help you take down the Netherbrain instead of running away.

Successfully persuading them to join you can make a huge difference, so pick your chosen stat for the roll wisely.

Make sure to use the Restoration Pod here to restore all your spell slots and health, too.

Walking through the archway will start a big battle in the High Hall Courtyard.

If you successfully persuaded the Watchmen to join you, they'll be right behind you as you head in.

You can also summon your allies here- the Harpers are particularly useful for back rank support in this fight, so they're worth calling if you have them. Allies will be automatically dismissed after a successful battle, but if you don't keep them alive, you can't bring them back.

The aim of this fight is to overwhelm you. Several enemies have the ability to summon allies - like the Winged Horrors and the Mistress of Bones - so before you begin a turn, go through the list of enemies and see which ones are a priority.

Items like Alchemist Fire are incredibly useful here. The Goblins can be annoying when they're all firing at one character, but they all have incredibly low health. Dedicate one character to taking out large packs of low-health enemies to make the fight much easier.

Remember, if you don't heal allies, they're gone for good. Spells like Mass Healing Word are incredibly important to use in this fight.

Once you've won this fight, save your game and heal up. Take a look around and see if there's any useful loot before continuing onwards. If you're not max level already, it's likely that your party will have leveled up again so take a moment to sort that.

You won't be able to use the Restoration Pod again (conveniently, it's been destroyed) or go to camp, but you will be able to take a Short Rest.

Heal up, loot, and save your game. Then, continue onwards east towards the Netherbrain.

You'll need to open the giant iron doors at the top of the staircase. This will reveal a brain stem that you'll need to climb in order to get close to the Netherbrain.

Unfortunately, the brain stem isn't tall enough. You'll need to take the staircase to the right of the brain stem to get higher up.

This will initiate a battle on the staircase with followers of Bhaal, Intellect Devourers, and a Nautiloid ship with a scary amount of HP.

Watch out for the glowing circles on the ground. When it's the Nautiloid's turn, it will use airstrike missiles to light up these areas and these attacks hit hard.

You only need to get one member of your party to the double doors on the top floor. When you get there, a cutscene will play showing dragons taking down the Nautiloid ships. The Absolute will speak to you with frustration, telling you that you're persistent and that you should leave your party.

There's a Restoration Pod here, along with a Gilded Chest that contains a few handy battle items. Make the most out of these, save your game, then climb on the brain stem to continue.

This will officially start the Netherbrain fight.

Netherbrain Boss Fight

If Gale is in your party, he will discuss the Crown with you, then your party will continue upwards to begin the boss fight.

The Netherbrain will acknowledge and mock your party, then summon a group of enemies to take you down. If you're a fan of save scumming, now's the time to do it.

Your aim here is to take control of the Crown of Karsus, which means you'll need to get close enough to it for The Emperor to successfully cast the control spell on it. When the spell is cast, you'll have direct access to the Netherbrain.

One of the most important things to note right off the bat is that there are counterparts for each one of your party members. For example, there is a Counterspell Wizard for Gale if he's in your party, meaning there is a character dedicated to stopping Gale in his tracks.

You're going to need to walk up the side of the brain to get to the Crown. If you stand on the surface of the brain, you will be blinded and tentacles will spawn. The tentacles are particularly annoying, as they can grapple characters.

Alongside the tentacles, doppelgangers, and Mind Flayers, you'll need to contend with additional Mind Flayers and Intellect Devourers. Additionally, a Nautiloid will pull up after a few turns and you'll need to start avoiding missile attacks as well.

Remember- missiles are launched at glowing circles on the ground. Avoid standing anywhere near them as they have a knock-back effect and can send you flying.

Get The Emperor to the Crown as quickly as possible. He will need to channel the spell to open a portal for a turn, so take out the nearby Mind Flayers and avoid bunching up as the Dragon will target groups with its Flame Breath attack.

Once you're inside the portal, attack the brain and avoid standing near the glowing orbs. You can jump from platform to platform or use abilities like Misty Step.

The fight inside the portal isn't particularly tricky. As long as you avoid the orbs, you can just beat on the Netherbrain with ranged attacks and projectiles.

As the Netherbrain loses health, it will start to take away different sections of the battle arena. If you're standing on a section that gets removed, your character will instantly die. Don't panic if this happens, though, your spirit will be available nearby for other party members to resurrect.

Once you've whittled down the Netherbrain, it will attempt to beg for its life.

Here, you've got a choice to make. Do you want to destroy the Netherbrain- and by extension, destroy all Ilithid tadpoles, freeing yourself, your party, and Baldur's Gate? Do you want to rule the Netherbrain with The Emperor? Do you want to betray everyone and become The Absolute?

Your choice here is crucial and it will dictate the end of your story. We went with the first option for our first run, fulfilling the initial goal of finding a cure and being declared as the Hero of Baldur's Gate.

Whichever choice you make here, you'll get to see it play out.

You'll see the impact of your choice on Baldur's Gate and its citizens - whether this is good or bad - and your party will react to your choice as well. The end credits scenes are quite long, but they're really worth sticking around for as they wrap up everyone's story.

There's even a post-credits scene featuring Withers.

With that, you've finished Baldur's Gate 3! Now, all you need to do is decide which type of character you're going to make for your next playthrough... might we suggest a Dark Urge Drow Ranger?