Head to Nchardak together with Neloth and take a look at the Black Book hidden beneath the floor - no magic is capable of getting it to the surface. The only way of obtaining it is using the mechanisms of the building. In order to do that, you have to head down to the Great Chamber, the entrance to which will be opened by the mage. Take the elevator down and get ready for a really loooong exploration.
Follow the mage and listen to his monologue. You will learn that in order to restore energy to the upper level you will have to turn on the pumps. They can be activated only by using the Control Cubes - unfortunately Neloth has only one, while you will need as many as five of them. You will have to find the others (which pretty much limits to following the mage and listening to his orders).
Head to the location pointed by the mage and use the Cube on the pedestal. That way you will open the door leading to the Nchardak Workshop. On the left side of the room you will find another pedestal with the second Cube (and a mechanism setting off a fire trap). Pick up the device and head deeper into the castle. Below you will come across two Dwemer Spiders - they won't pose any threat to such a powerful team as yours.
Cross the platform and put the Cube on one of the two pedestals at the end of the room. That you will clear the room of some of the water (its level will fall) and will be able to go down to the ground. By doing so you will however also activate two Dwemer Spheres and one Spider - don't worry, as Neloth will deal with them on his own.
Afterwards go down and put the Cube on the red pedestal - that way you will unveil a staircase leading to the upper level (which won't cost you the device, as the red pedestals don't "hold" them). Head to it through the passage on the left and... defeat the large Dwemer Centurion who will come to life.
Place the Cube on the best button to raise the drawbridge which was blocking the passage and head to the next room together with the mage. Take a look around the pick up the next Cube from the room on the left (it will also activate four Dwarven Spiders). Defeat the enemies and return to the room where you fought with the Centurion.
Head to the other side of the room and open the door. Neloth will tell you that reaching the further part of the dungeon is possible only with the water on a higher level. Return to the blue pedestal where you left the Cube and pick it up. Afterwards swim through the neuralgic point and head to the next room.
Inside there are two Dwemer Ballistas and a Dwarven Spider. Eliminate the threats and head to the small niche on the right to find another one of the Cubes. Pick it up and the large Centurion standing behind you will attack you (and the whole room will be flooded as well). Kill the giant enemy and head up the stairs - there you will find a red pedestal onto which you should put the just obtained Cube.
Cross the lowered bridge and return to the main room of the fortress (Nchardak Great Chamber). Approach the two pedestals (those which you saw at the beginning) and place two Cubes on them. That way you will lower the water level, but also summon a group of enemies - two Dwemer Spheres and a couple Spiders. Kill them and head to the lower level, which was flooded before. There, defeat two Ballistas and enter the location known as Nchardak Aqueduct.
In order to cross the aqueduct, you will have to lower three draw bridges. They can be controlled by a special mechanism placed right behind you, by the stairs. Enter the control room and take a look at the three buttons. In order to solve the puzzle, you have to place the Cube on the pedestal on the right and then on the left one (screen above).
Activate the machine to lower the bridges and launch an attack on the room - Spiders and Spheres will start coming from everywhere. It's best to let Neloth go first - he's strong enough to be able to deal with every threat (plus he's immortal). After getting rid of the enemies, cross the three platforms to reach a room with a blue pedestal (on the right). Place the Cube on it to lower the water level. The mage will now leave you - you will have to cross the rest of the location on your own.
Go below to the part of the room which was flooded up until now. Use the Cube on the pedestal in front of you and go through the door. Look out for the trap in the floor in the middle of the room and stand in front of the swinging blades. The easiest way of getting past them is using the Whirlwind Sprint Shout, though it's not required. Once on the other side of the dangerous mechanism, use another Cube on the next button and head to the small room with the last, fifth Cube. Look out not to step onto a trap when picking it up - poisoned arrows aren't anywhere close to being nice!
Return to Neloth and take the Cube which you have previously left in the Aqueduct. Before leaving the room, head into the room in the north-east to find a Kagrumez Resonance Gem which will come in handy in the unmarked mission Kagrumez (see the proper chapter of this guide).
Return to the Great Chamber and place three Cubes on the pedestal by the pumps - that way you will lower the water level. Afterwards pick up one of the Cubes from the upper floor and place it on the pedestal beside the last, fourth pump. That way you will unlock access to the Black Book. Before being able to reach it, you will have to fight a large Centurion who you have woken up with your actions. After defeating him, take a look around the room in which he was sleeping - there are some treasure to be found there.
Notice! At the very bottom of the chamber, there's a secret, locked and flooded room. In order to reach it, turn on the two pumps and head to the small room which has been unveiled therefore. There, place another Cube on the proper device and head onto the shallow ground. Inside one of the towers you should find a door activated with the red pedestal (if you're missing Cube, take one from the upper level). Head inside the room and take the artifacts.