After raising The Resistance level once again, John will send his capture team to you and you’ll wake up inside his bunker next. After the scene, you should be able to control your character. While still bound in the chair, move to the doorway and fall down the stairs. This should set you free.
Start by crawling under the pipes and through a pipehole. Drop down then crawl through another pipe hole again to reach the barracks of the cultists. There’s a baseball bat as soon as you emerge that you can use for silent takedowns. Stealth is necessary here since you’re in enemy territory. Start off by silently taking out the cultists here and taking their weapons. Make sure to craft explosives and homeopathics as you collect materials. While in the barracks, go up the blocked stairs to find a medkit, a smoke grenade, and some ammo.
Leave the room and continue to the next corridor. Carefully take out the two peggies there and continue until you reach a blast door. Open it and continue to the next corridor. Both corridors lead back to the same room but carefully head left first. There’s a couple of peggies talking so wait for the other one to leave then kill them silently consecutively. The other end of that corridor, beside the doorway that’s marked B1, (with some boxes and flowers) is a locked storage room.
The key is found beside the TV by the stairs, inside the barracks. Be careful though since there’s a lot of enemies here, including two “angels”. These are resistant to damage but can be instantly taken out with Melee takedowns. The door leading to Deputy Hudson will be opened by two peggies that will arrive as reinforcements as you clear the area. Once clear, head back to the corridor and use the key to unlock the storage room. You’ll find ammo, body armor, smoke grenades, a magnum, and mustard.
After looting the contents, follow the mission marker and a cutscene will play as soon as you step in the chamber. After the scene, you’ll have to escape the bunker as it starts to fill up with bliss. Use a homeopathic to boost your damage resistance and run towards the stairs. Kill all enemies along the way until you finally reach the exit. There are angels outside so make sure to throw an explosive ahead of you to clear the path. Keep running away from the compound and follow the mission marker until you reach the road. Wait for a few seconds and the mission will be complete.