This Quest starts when you are return to the World Map after completing the Main Quest called He Waits In Fire. You'll receive a missive from Queen Onekaza asking for assistance with a final matter before undertaking the journey to Ukaizo.
You'll now be at #1 on the rooftop
of the Kahanga Palace. Speak to Queen Onekaza at #4. She wants you to infiltrate the Powderhouse of the Royal Deadfire Company, and level it with an explosion. She wants you to leave no witnesses behind. And she intends to have a witness she has in hand to implicate the Vailian Trading Company for the deed.
If Pallegina is in the party, Onekaza will insist that she leave before she fully reveals her plans. If you insist on Pallegina remaining, Queen Onekaza will end her alliance with you and this Quest will fail. That means you either have to make the trip to Ukaizo yourself, or find another ally among the other three factions. If you tell Pallegina to leave, she'll leave the party for good at this point.
Things will get similarly tense if Maia is in the party. She will want to leave if you express a desire to commit to Queen Onekaza and the Huana. It is possible to talk Maia into staying and seeing through this Quest to its conclusion. The dialogue requires ALL of the following:
Pass either a Diplomacy check of 5 or an Insight check 4, or have any points of positive reputation with Maia.
Complete The Courier's Calling Quest in a way that you learn that Maia is an assassin, and Tuama and Harama are still alive.
The front door to the Powderhouse is at #7 on the map of the Brass Citadel. The Guards at the door won't let you in, no matter what dialogue options you choose or what Skill checks you make. You could attack them, but that would turn the whole district hostile against you.
An easy way is to go near the front door of the Imperial Command at #14, and then go east along the battlements until you reach the door at #13. A lone Guard will be patrolling it. You can unlock it with either a Mechanics skill check of 15, or pickpocket him for the Powderhouse Key. Now you can walk in.
You'll be at the door at #3 on the map of the lower floor of the Powderhouse. You would have been come in at #4 had you forced your way in through the main door at #7 in the Brass Citadel.
The Guards will want you out if they see you. You can kill them straightaway. You can use Stealth mode to sneak past them, but that will be easier with a lone character or two with a LOT of Stealth skill. Or you can actually get run of the place if the Watcher can make a Bluff check of 12 and has at least 1 point of good reputation with the Royal Deadfire Company.
However you do it, the stairs at #5 lead to the Storage of the Powderhouse.
There will plenty more Rauatains in the area, so it's up to you whether you want to kill them or sneak by them.
Your objective is to place the Timed Explosive in the vat at #8.
You'll have limited time to leave the Powderhouse. If it blows while you're still inside, your game will end then and there.
Leave, and you'll see a cutscene of the Powderhouse being blown to smithereens. The party will end up in a random encounter area called "City Streets", from which you can travel elsewhere in Neketaka.
Travel for the main floor of the Kahanga Palace. Director Castol will be on trial for blowing the powderhouse, with Andaccio being the star witness for the Huana.
You can either deny having seen the explosion, or publicly admit you blew the Powderhouse. Either will cause Prince Aruihi and his Huana minions, along with Hazanui Karu, to attack you. Prince Aruihi leaves behind an Amuet of Greater Health, a Girdle of Mortal Protection and a Serpent Crown when defeated. This option means you fail this Quest, and rule out any alliance with either the Huana or the Royal Deadfire Company for purposes of completing The Coming Storm Quest. Your remaining options will be the Principi, the Vailian Trading Company, or sailing to Ukaizo by yourself in a suitable ship. In fact, you can now head over to the second floor of the Vailian Trading Company Headquarters and speak to Director Castol to seal an alliance and complete the Sabotage at the Brass Citadel Quest. However, you will still need to complete the Skipping Ahead Quest in order to complete The Coming Storm Quest.
The other course is to see through Onekaza's scheme by verifying Andaccio's testimony. Director Castol will be banished to the Gullet for the rest of his life, and his holdings being given to Hazanui Karu. That also means any remaining Quests for the Vailian Trading Company will fail, and rule them out as an ally for The Coming Storm Quest. You'll now get 40,000xp for completing this Quest.
You can actually at the last minute publicly admit you blew up the Powderhouse after Director Castol has been banished. The Huana led by Prince Aruihi and Hazanui Karu will attack you. The aftermath is that literally only the Principi or sailing to Ukaizo yourself will be your remaining options.
Queen Onekaza invites you to speak to her at the Rooftop. Note that at this point The Final Maneuver and A Dance With Death Quests are still open, and you have a last opportunity to ally with either the Royal Deadfire Company or the Principi through those quests. The former Quest involves assassinating either Queen Onekaza or Prince Aruihi at the behest of the Royal Deadfire Company. The latter Quest involves finding The Floating Hangman ship for the Principi.
If you want to ally with the Huana, now go up to the Rootfop and speak with Queen Onekaza to confirm it. It is at that point that the Royal Deadfire Company and Principi Quests now fail. It is also at this point that The Coming Storm Quest will now also be completed.
If you complete both this Quest and The Coming Storm in a way that seals an alliance with the Huana, Pallegina will now leave if she hasn't already. And that's even if you left her on the ship and not in your core party. She'll leave you with a letter, and no longer be part of your roster.
Maia will likewise leave even if you left her on the ship, that is unless you talked her into staying when you earlier spoke to the Queen.
If you complete this Quest to seal an alliance with the Huana, and killed any Rauatians inside the Powderhouse, then everyone in the Brass Citadel will attack you on sight.
The only way to avoid this is by having planted the Timed Explosive in the vat of the Powderhouse through Stealth and without killing anyone.
There is an alternative way to complete this Quest, and it allows you to keep Maia. Go through the door at #14 in the Brass Citadel.
You'll now be at #1 on the main floor of Imperial Command. Speak to Hazanui Karu at #3. She'll want you to agree to assassinating Queen Onekaza as part of The Final Maneuver Quest. The Hazanui and all the Rauatains in the Command will attack you. Maia will remain in your party during and after the battle, although she will refuse to speak to you afterwards.
Now speak to Queen Onekaza at the Rooftop. The conversation will mirror the one where she asks you to blow the Powderhouse up until a point. But the difference you can seal the alliance with the Huana then and there.
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