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Warhammer 40K: Rogue Trader

Where the Shadows are Deepest of All Walkthrough - Rogue Trader

Matt Chard

When you reach Footfall at the start of Chapter 2 in Rogue Trader, you’ll have a few different areas you can explore, with one of them being the Shadow Quarters. Here, you’ll find a place closed off due to a quarantine. If you speak to the “Extermination Brigade Sergeant” in front of the gate, you can start the “Where the Shadows are Deepest of All” quest. When you speak to the Sergeant, he’ll tell you that you’ll need to speak to the Liege. Agree to send help to the people stuck in the quarantine zone, and then you’ll be told to “Wait” before you can carry on with the mission. In short, you’ll need to complete the “Reclaim What was Lost” quest in Kiava Gamma first before you can continue with the mission, but if you’re wondering whether it’s worth investing your time into this quest, then read on.

How to Start Where the Shadows are Deepest of All

Head to the quarantine zone situated in the southeast of the Shadow Quarters, Footfall, and speak to the Extermination Brigade Sergeant“ in front of the gate. He will tell you that no one is going in unless the Liege says otherwise. Leave the Shadow Quarters, head to the Liege’s Residence, and speak to him regarding the matter. Ask him, “What is happening in the Shadow Quarters? Why is there a quarantine”, and he’ll explain why. If you’re playing an Iconoclast playthrough, you’ll have a choice to help the people inside the quarantine zone, which will reward you with +5 to Iconoclast. After this conversation, the quest will update to “Assess the Situation”, and when you read it, you’ll find out that you have to wait.

(1 of 3) Head to the southeast of the Shadow Quarters and speak to the Sergeant to start the quest.

How Long to Wait — Assess the Situation

The game doesn’t give you a lot of information on how long you have to wait, but after some testing, it becomes available once you complete the “Reclaim What was Lost” quest in Kiava Gamma, so you will need to progress through the main story until you’ve completed it. Once you’ve accomplished this task, make your way back to the Shadow Quarters, and head back to the quarantine zone. When you get there, you’ll notice that the gate is open, and the whole area is free for you to explore. Now, you’ll need to find the Mutant Lair.

How to Find the Mutant’s Lair

As you walk down the set of metal stairs, you’ll get an Awareness check of 36. If you pass it, you’ll find a magnifying glass on the wall next to the pipe. Interact with the magnifying glass, and you’ll find some residents hiding. You’ll get a few choices here, all of which are some variations of open-up. After listening to what they say, you can verify their claim or blow them up. The choice won’t have any impact on the story, but it may weigh on your conscience, so either save them or kill them, either way, you’ll find out that there are mutants below.

Now, this doesn’t really help you find the location exactly, but it will “allow” you to find it. The Mutant’s lair is in the same area, at the mouth of a large pipe, opposite the dilapidated house in the center. This will require you to interact with the [Awareness] magnifying glass, and if you pass the check, the entrance will open.

(1 of 4) In the quarantine zone, make your way down the stairs and check the magnifying glass icon on the wall.

Deal With the Mutants - Mutant Encounter Guide

Enter the lair and prepare for the incoming battle against a horde of mutants. This encounter is relatively easy, but you will need to be quick at dispatching them as the mutants will spread the disease around the arena causing Toxin damage. The best way to deal with Toxin is to use an Adaptive Antidot on each party member, as this will grant you immunity to Toxin for the rest of combat at the cost of -10 "Toughness" iconToughness.

At the start of the prep phase, split your party, and place them on both sides of the cover (left and right), preferably with someone who can take a hit. For the rest of the party, have them stay behind the cover at the entrance of the room, and take the enemies out from there. There are a lot of enemies here, but fortunately, most of them will go down in one or two hits. When you defeat a mutant, it will explode, leaving behind a debuff called “Shadow Quarters Disease’’. This nasty debuff will give you three stacks of the disease, dealing minor damage on a hit before the stack resets, so ideally, you will want to defeat the enemies from afar, but with the Antidot, you should still be fine taking a few hits of it.

(1 of 2) Use the cover near the entrance, and use Antidots on the entire party, and then take out groups of the mutants with grenades.

Use the cover near the entrance, and use Antidots on the entire party, and then take out groups of the mutants with grenades. (left), Defeat the Mutants quickly, otherwise they will spread the disease around the entire battlefield. (right)

There are some Mutants that have the same name as the other enemies but will have five times the health. This variant will get up into your face, and attack you with their knife, applying Toxin on hit. Although these take a few more hits to defeat and deal a bit more damage than the standard variant, they shouldn’t cause you any problems. Finally, there are Mutant Infectors who have the ability “Pus Grenade” which is basically a Toxin grenade. Ideally, you will want to take these down first, as they can hit multiple party members at once. One of the more frustrating aspects of this battle is when the enemies use “Spread the Disease”. This will place Toxin around the area which will slowly take over the whole arena dealing…you guess it, Toxin. This is why you need to defeat the enemies quickly, otherwise, you can get overwhelmed.

The easiest way to deal with this battle is to use an Antidot on all party members, use a Warrior to use a taunting scream on as many mutants as they can, and then throw a grenade or two at the group to take them out. This leaves your Bounty Hunters to take out the stronger variants as they can debuff them and defeat them with a few well-placed attacks. In all honesty, this battle isn’t too difficult provided you can take them out quickly, and you have Antidots. Once they’ve been defeated, the quest will finish, and you’ll receive a large amount of experience points for completing it.

All Shadow Quarters Quarantine Zone Loot

Here you will find where to acquire any noteworthy loot. There are other chests containing goods around the area, but these will just have random cargo in them.

  • Pyromaniac Boots: In a large crate by the sewer pipe in the alley after you walk down the stairs. It’s in the northern part of the southeast section of the map.
  • "Toxic Knife" iconToxic Knife: Requires you to pass a 69 Awareness test. The weapon can be found inside some lockers in the area with a large fan in the center, just beyond the gate where the Sergeant is. It will be on the right side of the room.
  • Old Tunnel Cache Clue: Near the Pyromaniac Boots, there is a sewer tunnel that has some rubbish in front of it. Pass the [Demolition] check to destroy the rubbish and find the clue. This clue will lead you to the cache (Dreams and Stories quest).
  • "Imperial Pride" iconImperial Pride (Bolt Weapon): On a dead body (not an enemy) on the floor in the center of the Mutant Lair.
  • "Stimm" iconStimm x3 and an Intoxicating Elixir: In a bag under the shed in the Mutant Lair.
  • Packing Reagents: Obtained from one of the stronger Mutants in the Mutant Lair.
  • Lots of Cargo: There are a lot of cargo goods to pick up in the Quarantine Zone, and the Mutant Lair.

(1 of 6) You’ll need to pass an Awareness check to find the Toxic Knife.

More Rogue Trader Chapter 2 Guides

If you’re having any trouble with any other quest, puzzles, or battles in chapter two, check out the guides below.

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Guide Information
  • Publisher
    Owlcat Games
  • Platforms,
    PS5, Steam, XB X|S
  • Genre
  • Guide Release
    23 November 2023
  • Last Updated
    8 March 2024
    Version History
  • Guide Author

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In the grim dark future of the 41st millennium, there is only war. The Imperium of Man, ruled by God-Emperor of Mankind from atop his Golden Throne, is a vast interstellar empire with countless armies. Despite the Imperium’s apparent strength, however, its enemies are even more numerous and threats to mankind both surround the Imperium and gnaw at it from within. Where the constantly strained military might of the Imperium can’t reach, humanity must find other champions, and blessed with holy Warrants of Trade, Rogue Traders have almost unlimited authority to operate in the unconquered reaches of the galaxy beyond the Imperium’s direct influence. After unexpectedly inheriting the title of Rogue Trader von Valancius, you’ll have to secure your holdings in the Koronus Expanse, establish and develop new colonies, investigate the conspiracy that led to your ascension and fend off threats, internal and externals, humans, xenos and worse…

This guide will provide the following information:

  • Tips and info about various gameplay mechanics, including injuries and trauma, veil degradation, momentum, resolve, heroic acts, weapon types and space exploration.
  • Recruitment guides and builds for every companion in the game.
  • Walkthroughs for main quests, boss battle strategies and the effects your choices have.
  • Complete chapter overviews.
  • Best weapons lists for each chapter.
  • Guides for optional dungeons, side quests, errands and solutions to puzzles.
  • Colony guides, including colony projects and their rewards.
  • A vast database of weapons, armor, accessories, abilities, talents and more!

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