As the Sewer has become contaminated with toxic fungi due to the damp environment created when the underground spring runs dry, you will need to be vaccinated with blood from a corpse located in the Morgue in order to pass through unharmed. The sewer water must be redirected to the Cistern before accessing the Sewer.
Brutes patrol the Sewer and it appears one tore down a gate blocking one of the paths.
As noted above, you will not be able to enter the Sewers until first redirecting the water in the Cistern , and creating and receiving a vaccination from the Morgue. Attempting to do so will result in Daniel taking damage from the fumes, and a message stating that he cannot continue without adequate protection.
After entering the Sewer, and climbing down the ladder, a Brute will be seen a little bit down the tunnel. The first Brute encountered in the Sewer is mostly harmless, walking by the end of the entrance tunnel, similar to the Servant Grunt encountered in the Archives. It is purely for cinematic purposes and will disappear if you approach it too closely.
The end of the passage opens out into a larger area with two paths to the left and right, and a spinning metal wheel in the center, the purpose of which is to channel the water. It is inadvisable to touch it as this will result in injury.
Take the path to the right until you come to the end where a broken pipe is sticking out. Grab it and move it up and down until it breaks off, then take it with you. Head back to the wheel area. You cannot jam the wheel with the broken pipe just yet as the blades are spinning too fast, so head down the left path.
In one caved-in passageway a Kaernk may be heard trapped in the rubble. At low sanity, Daniel might also hallucinate a Kaernk, but it will not attack him. Continue along the path until you come into the room with the machinery powering the wheel. In order to make the wheel run at its slowest, pull the lever marked I to the left and the lever marked II to the right. The noise will lower considerably. Beware! As you leave the machinery room, a Brute will spawn at the bottom of the stairs and stay for awhile outside the door, so just run back, close the door, and hide in the room.
You can now jam the now slowly-running wheel with the broken pipe. Crawl under the wheel into a new area of the Sewers and enter the room to your right.
The Shadow often roars if Daniel takes a wrong turn and proceeds down a dead end. Its most prominent appearance here is in a room in this next part of the Sewers, where the Shadow, besides leaving its fleshy calling card around, also savagely slaughtered a Servant Grunt. The young man will lose some sanity at the sight and Alexander will become frantic as the cosmic force kills his servants, demanding Daniel turn back. As you attempt to leave the room, a Brute will spawn. You have two options, the safest of which is to hide in the far rear of the room behind the doorway where the Shadow caused a cave-in. The Brute will break down the door to the room, but as long as you are hiding in the rear and avoiding looking at the monster, it will eventually leave you alone.
The second option is to flee back down the steps and run back through the jammed wheel, as the Brute is unable to break through it. However, this is riskier as the monster will see you and give chase.
Once you feel safe, exit the room. You will see that the Brute has torn down some iron bars that obstructed your path before, so head down that path.
You will see a Brute guarding the only way out of the sewers. The monster will not simply walk away, so it must be distracted. A group of rocks are on a drain spout to the left of the entrance to that section. If you go forward and turn right, you will see another drain spout with a bunch of rocks and a laudanum. Take one rock from either section and throw it depending on where you took it: if you took it from the first drain spout, throw it to the left of the monster. If you took it from the second drain spout, throw it to the right of the monster. Immediately after throwing the rock, run the opposite way around and dash through the path the Brute was guarding. The Brute will immediately realize it has been tricked and will pursue you. The strategy just described leaves you just enough time to pass through the door without having to close it. The second door spawns another brute when you come near it so you must open it fast and either close it or climb the ladder you see as fast as you can. If you want to buy more time, do not run the opposite way after throwing the rock; simply dash past the monster as it investigates the source of the noise and close doors behind you to slow both down. Again, this is riskier because the Brute can kill you with a single slash if it sees you.
Departing this area will cause the Shadow to bellow angrily as the man it wants has escaped it again. The ladder starts to break as Daniel arrives in the Nave.