After the long trip down from Devil's Reef, you reach a small underground city. After a save point, and a short trek, you will see Sebastian Marsh arriving by a portal.
If you want to hide, there's an alcove directly ahead, but this is not required as there aren't many sentries present. The main route leads to an obvious dual-portcullis trap to contain you, and where Sebastian Marsh has his minion throw you in a prison.
When you wake up in the cell, you have visions of a few nearby sentries. First, collect the chisel on the ground, and use it to pry the sewer grate at the bottom of the cell. When you move to the other cell, climb up to disturb the fish man, and climb back down to hide. One sentry will enter, beat the fish man, and close the door behind him. He will also wander away from the door as well.
Outside the cells, there are four sentries to evade. Two remain still, and the other two are in a small patrol route. Outside the cell, advance slowly, and watch the sentry on the left. Advance to the right when he turns away.
The second will be visible when you approach a branch. When that sentry turns away, enter the branch, and turn left into the crawlway before the stationary guard. Wait for the moving sentry to move away, then continue down the path.
You'll reach the first sentry patrol route again. Wait for him to turn away, and head into the third corridor and into the crawlway. You can save here, and exit the prison.
Continue to the left. There are two guards at a campfire. Circle around to the left. When you're about to approach the path leading up int he open, you may see a temple guard on the path far above. Wait for him to return, and continue up the path. You will need to follow him, and sneak past them. Although the two guards would be facing you, staying close to the wall will allow you to pass easily.
In the corridor leading to the temple entrance, look for a crawlway to the left. This lets you reach the temple entrance more easily, but it is bolted shut and you need to sneak to the other end of the cave.
This will lead to a garden, where you can retrieve a blue plant. Pick it up, as it is needed later. Continue to the crawlway in one of the walls.
This leads to a crystal cavern, where you see a green crystal but can't collect it now. However, there is a save point you can use here.
The path leads to a waterfall area. Climb down the side, and to the bottom of the waterfall. There are two paths,. You want the one on the left, not marked by the medikit. Climb up this route, up the path until you reach a save point before a ceiling grate.
When you approach the grate, you will see Robert Marsh, first talking with a temple guard, and then get into an argument with Sebastian Marsh about how the order should proceed. After the ceiling grate collapses, Robert Dagon will start his attack.
To kill Robert Marsh, you need to retrieve the knife on the desk, found to the right of the chair. You will also need to evade his attack, handled by crouching behind a solid object as he tries to draw you forward. When he's recovering from his pull attack, use the knife's aimed mode, and stab to kill Robert in one hit.
Open the briefcase left by Sebastian to collect a book and the key to the laboratory.
You can exit, but the hallway outside has four guards. When they aren't looking, head to the right and down the stairs, where you can get a bolt rifle and a medikit. Return, and aim for the smaller guards with the firearms first. The two sorcerers can be dispached second.
Continue until you reach the door. You can shoot thorugh a crack next to the door to soften up the guards, before unbolting and returning to the first chamber. The main chamber is reinforced by two more guards, which are two fish men on patrol. Head into the side corridor, and unlock the door to the laboratory.
In the laboratory, can collect a chemical weed killer and a paper on the blue flower you picked up in the garden. You can also speak with a genetic experiment for information on how to reach the temple. For now, you need to return to the prison, accessed through a second door.
The prison sentries will most likely be active when they spot you, but you can fight back with your rifle. You will first want to head down the middle of the prison, where you can collect your previous weapons, and a prison feed bucket. When you open the door, eliminate the four sentries to ensure you are safe.
In the prison is a second bolted door, which is a cell to a Beloved. You need to poison it, by placing the blue plant (found in the garden between the temple entrance and crystal cave) and feed bucket (found in the center of the prison) into the feeding slot for the room. When both items are in, close the slot, and the beloved will poison itself and die. You may now enter the room to collect the hammer.
Yithian Lightning gun
Return to the crystal cave, and use the hammer and chisel to retrieve the green crystal. When you try returning, you will be attacked by fishmen coming out of one of the walls.
Return to the second floor of the prison, and use the chemical weed killer on the dangerous-looking plants. This allows you to climb the vines into a chamber. Insert the green crystal into one of the slots, and find a button to activate a machine. This opens a portal that leads to the waterfall source chamber, and where you can retrieve the Yithian lightning gun. This weapon has an effectivly endless power supply, and can kill most enemies in one hit.
With this weapon, you now need to find the hidden path to the temple. Exit the waterfall source cave by taking the passage to the left, and defeat any opponents you come across. Head to the waterfall chamber, and follow the path to the right, which contains starfish blocking the path. Fire the lightning gun at the water to fry the starfish, and continue to the end of the path.