Large Crypt
Your first real puzzle comes in the room we'll call the "Large Crypt". You enter a door and run down a long ramp. In this room there is broken masonry on the floor, and a barred gate on the opposite side of the room. Switch to Spectral/Etherial form, and you will encounter your first Etherial Vampire (Wraith). Kill it, and notice that the shift to the Spectral plane has created a warp in the wall which allows you to climb up into the rafter-area of the room.
After climbing up, shift back to material form. Use the t-shaped rafters in front of you to get to the left wall (or you can jump and glide). You need to open the barred gate in this upper area. To do this you need to put the large block on the left wall into the alcove behind it. This is acomplished by "flipping" the block over the ledge. You will be using the "flip" frequently to manipulate blocks or stack them on top of each other. To flip a block, press and hold the "L1" (crouch) button, then hit the square (action) button.
After the upper gate opens, enter the next room and high-jump/glide to the rafter you see in front of you. From this first rafter, you will notice two platforms attached to wall-ropes on either side of this room. Jumping on them in material form will cause them to drop. You want to have one of these plaforms raised high enough that you can use it to jump to the second rafter IN ETHERIAL FORM after you are done with this room's puzzle. Jump on one of these platforms and ride it down to raise the other one. The exit of this room is up in this higher level, on the opposite side. But you need to open the exit gate first.
The key to opening the gates is in the lower area of this second room. You need to get the block in the far wall into the alcove in the wall you entered through. Don't bother trying to flip the block up onto the small ledge on the side of the room: for some dumb-ass reason, the game won't let you. Instead, you have to move the block though the pit in the center of this room. You may want to repeatedly jump down into the center of the pit to kill all the zombies that appear from the mounds of dirt before you move the block. Push the block to get it down, then flip the block to move it up the ledges on the other side. After you get the block into its alcove, shift back to the Spectral/Etherial plane, go through the now-open lower gate, climb the wall in the first room, then high-jump/glide across the rafters and platform in the second room to exit.

In the next room you will find two blocks. Your objective here is to match each of these blocks into their respective holes in the wall (alcoves). The real trick to this puzzle are the two blocks stacked atop one another. In order to use the blocks you must find a way to separate them. We suggest moving these blocks to the corner across the room that has a ledge protruding. Once the blocks are near the ledge, jump to this ledge and shove the upper block off onto the floor. (You may also be able to separate them by pushing one into an alcove and letting the other one fall.) Don't forget the flipping technique if you need it: L1+square while facing a block. Then line up the symbols on the blocks with the symbols in the alcoves, and push the blocks in.

Pass through the gate to a set of double doors. Go outside of the double doors and to the right you will see a block. Push this block forward and off the ledge, down to the ground below (make sure you push the block first, before jumping down, otherwise you'll have to go all the way around and back to this area). From here you will want to jump down below by the block and move the block by another block already on the ground. Flip the new block atop this one and drag the stack to the right against a white pillar. Now climb atop these blocks and high-jump to reach a new triangular pathway.

Travel through this triangular passageway until you reach another greenish lake, only this time much smaller. Move your way around this smaller lake and up to the small building above. Go inside this building and travel the corridor until you reach two screwlike pillars protruding from the ground. Kill or evade that nasty vampire (there's another killing-staff in the room behind him, if you want it).

Now find the elevator-like contraption against the far wall. Move onto the metal grate of this elevator and hit the arrow-switch on the wall (you'll be coming back to the lever behind you later). The elevator will take you to a lower level and from here you will begin a large puzzle.

Engine Room

You are attempting to break into Malchia's stronghold. Go through the entrance area, up the stairs, kill the dirty hu-man, and enter the engine room. Staying on the upper ledge of this room, activate the switch on one side and turn the crank on the other.