**Note: If you have horses you do not want to bring them here. You will lose them when the Filth Factory explodes, so it's best to leave them in Hectar or Shayder. Thanks to Dave for pointing out that I should probably include that little tidbit**
Upon first entering the Filth Factory you'll find yourself facing what appears to be a solid wall, but you can actually just walk through it. From here I'll be following the map in a counter clockwise direction.
The first room is pretty much empty, though there's a door to the east that leads to a viewing chamber for the lower floor. All you can see is blackness, however. The door in the northwest corner of the entry room leads to a stairway leading down, but it's been blocked off by a lot of rubble. In fact, all the stairways leading down have been blocked off in this manner.
Now head out the southern door. This leads to a room with two pits in the middle. You do not want to go into those pits, as theyll give you a very bad illness. Head into the passage in the northwest corner of the room to fight a few roaches.
The other door out of the room leads to the south into a passage that extends west and east. Go towards the west. When you enter the laboratory stay well clear of the sphere in the center of the room, as it will disease your entire party. There's a roach in each of the holding cells to the south, and the door to the north leads to a small room containing a one use sphere which will cure your entire party.
Head back into the passage and to the east. The passage will split, going north and south, with a short passage leading to the east. Avoid the short passage and clear out the roaches to the north and south, and then go into combat mode before going east. There are two giant slugs in a pit in the middle of this room, and you want to kill them before they attack you, since they'll spit acid on you, and acid is kind of hard to cure.
Once you've killed the slugs go through the door in the southeast corner. You'll find yourself in a short hallway with three doors to a side. All of the rooms are empty except for the last one on the southern side, which contains a Basilisk, and the middle one to the north, which contains two mirrors. Be prepared for combat as soon as you open the door to the Basilisk room, since you want to either be standing next to it or, even better, have killed it before it gets a chance to attack. Basilisks will sometimes turn you to stone when they gaze.
Take one of the mirrors and head towards the northeast corner of the room where the slugs were. Open the door and push the mirror into this large room. There's a single roach that wanders around in this room, so don't be surprised if it pops around one of the corners at you. Leave the mirror by the doorway and go to the north along the eastern wall. You'll see a laser blocking a chest, so bring the mirror over and push it into the lasers path to redirect the beam, allowing you to reach the chest. There's a second chest in this room, just south of the door you came in through, but unless you have Move Mountains Lv.3, which is rather unlikely, you can't reach it.
Go through the room and out the door to the north. This is a pretty empty area, though on harder difficulty levels I've sometimes found that one or more of the monsters from the next room has somehow developed opposable thumbs and come through the doorway. There are two doors along the eastern wall. The first leads to a roach, and the second to an empty cell. Take note of the door in the southwest corner and then go out the door to the north.
You'll find yourself in another room with a pit in the middle, this one containing some Spore Beasts and some Cave Slimes. Once you've killed them take note of the door in the western wall, then head out the passage in the northwest corner. There's several side alcoves along here containing roaches.
The passage ends in yet another room with a pit in the middle. This one contains Spore Beasts and Roaches. There's a passage in the southeast corner that leads to another viewing chamber, and a door in the northwest corner that leads to three chests. Check the chests for items, then go back to the second pit room and through the door in the western wall.
You should be in a small room with a teleporter. You can only send one person through the portal, and you're going to have to fight some monsters and unlock a door on the other side. It's your choice who you want to send through.
Upon first arriving on the other side you'll be in a long curved hallway. Head down the hallway and a section of wall will open up revealing some undead. While you're fighting them a few roaches will come around the corner and attack you. Once they're all dealt with go to the end of the hallway and through the locked door.
There's a Guardian Roach in this room, and they aren't exactly easy, especially for a low level or weak character. Once you've killed the roach check out the bookshelves on the northern wall for a couple Research Tomes, and read the book on the pedestal for some information on the Factory.
Go throgh the door to west to find a few more roaches and yet another blocked stairway. Now go back into the room where you fought the Guardian Roach and approach the control panel in the northwest section of the room. There are four buttons on the control panel, but you only need to be concerned with two of them. For now press the one that says Release Swamp Scavengers and then go back to the portal to rejoin your party.
Check out each of the three rooms that have pits in the center, and you should find that in each room a section of wall has slid back to reveal two Spore Beasts and a Shambler. In addition, the rooms that originally had the Spore Beasts have secret areas in the back of these new areas with a few items.
Head back to the portal and send whoever you want through to return to the control panel and press the Deactivate Power Conduits button. Now you have to move quickly to reach and get through the power conduit before the power comes on. As long as you don't take some really long side trips you'll make it with time to spare.
Once you've pushed the button go rejoin your party and then head into the room to the south of the pit. Check out the southwest corner of the room, where I told you to take note of the door earlier. Go through the door and down the passage until you reach the portcullis. Through here is the power conduit, which you just deactivated. Cross it quickly and go through the door at the southeast end of the room.
In here you'll find the body of an Avernite, who you can loot for some decent items. Then go around the corner and find the ladder leading down to the Lower Filth Factory.
Upon first entering the Lower Filth Factory you'll be in a short passage leading to the south. Follow the passage and go through the door into a short hallway.
The first door to the west contains a room with three levers. Without touching any of the levers, read the three signs that say what they're for.
The first door to the east leads a small room with a rune in it. I've never quite worked up the nerve to put someone on the rune and use the corresponding lever across the hall, but I've heard the results aren't pleasant. The next room is just a small empty square that has apparently been walled off recently.
The next room to the east contains either some Poison Fungus or some Spore Beasts, I've never been quite sure which. There are two cells in this room with three of the beasts in each cell. You can either kill them through the portcullis, or you can go across the hall and use the corresponding lever to raise the portcullis'.
Head through the one remaining door and you'll find yourself in a room with a lot of barrels and a lever. Pull the lever and then go back to the room that had the three levers. Pull the middle one and then wait a while until you hear a big explosion. Go back into the room where the barrels were and there should now be a big hole in the wall, exposing a teleporter. Step into the teleporter and get ready for the final section of the Filth Factory. Be aware that there are a variety of Roaches and Guardian Roaches wandering this section of the Filth Factory, so expect to run into them at any time.
The first thing I usually do here is make a lap of the outside section of this level. There's portals in each of the four corners, but all they do is lead to each other. Along the southern section of passage is a side branch to the north which is blocked by some stalactites. You need either Move Mountains Lv.2 or a Stoneshatter Crystal to get through here. The crate at the end contains some decent items, including an Archers Ring.
Once you've done a lap go just a little bit west of the first portal and check the southern side of the wall for a passageway leading inwards. When you first get out of this small passageway you'll find yourself in the main processing pit of the Filth Factory. It's probably a wise idea to use the Safe Travel spell if you haven't gotten at least 5 Pathfinder for each of your characters from Meena.
Just to the south of where you came out are the beams that heat the filth that makes the walls. Stand near the beams and check the ground for some Healing Herbs, then head around the outside of the wall. Near the center of the western wall is a paved area with a passage leading upwards to the exit. You don't want to go up there yet, but you definitely want to remember where it is.
In the far southwest corner are two rooms. The first room contains two puppies, so I try to avoid going into that room, since it bothers me to see them, and the second room contains some undead, which you can kill.
Head down to the southeast corner to find some small side passages with roaches. The most northern of these side passages has a body at the end of it, with some pretty weak items, but you need Move Mountains Lv.3 to reach it.
Now go back to the main area and continue until you're standing on the southern side of the Power Conduit. Check the ground here for some Spirtual Herbs.
Head all the way back to the center of the western wall and enter the middle section of the Filth Pit. Make your way around this circle once, then go to the center of the eastern section of this inner circle.
Check out the next ring, paying special attention to the southern wall. There's what appears to be a broken Laser here, with some evidence for you to take to Berra inside. Make sure you pick this up before breaking the Phoenix Egg, because once you do that you won't have time to stop and pick anything up if you want to make it out before the Factory explodes. And once the Factory explodes, of course, it's gone, and you won't be able to get back to it ever again.
Once you've done all this, go to the very center of the Filth Pit, the entrance of which is in the center of the western side of the inner circle. Break the Phoenix Egg and then run to the exit I told you to take note of near the center of the western wall.
Go up the passage and out of the Filth Factory. Then go back to Shayder and tell Mayor Berthany to get your reward.
Don't forget to go back to Upper Avernum to tell Anaximander you've completed the Roach Quest, and to the Tower of Magi to get Lightning Spray Lv.3 from Solberg as your reward. Talk to Levy to get a Ring of Skill as your reward. It's around now that Anaximander should give you a quest to recover the Orb of Thralni, that's been stolen, and also when he'll give you the Jewel of Return.
Also, next time you're near the Inn of Blades in Krizsan Province, stop in there and tell Oralse about killing the roaches for a reputation point.