In the very begginning, take a left out of your prison cell and go through the door to execute James Cavanagh.
When you get out of the vents, take a left and go through the door to reveal a kevlar suit.
No real secret areas, the only cool spot is that cave behind the house at the bottom part of the cliff.
All three nalis in this level open secret areas. So be sure to follow all of them and stop them from being killed, the easiest way to save the last nali is jump over the river of lava so the brute fires away from the nali when it spots you. After you kill it just use the broken beam to make your way up.
This area is right when you leave the start. When you find the corpse with an automag, go straight. Just be sure to grab a couple of flares or use your dispersion pistol for light. At the very end of this pitch-black tunnel you will find something rather useful.
First shoot the explosive barrel to make a hole in the wall, then run and jump against the slope.
In order to get this shieldbelt, you must NOT let the first nali that you come across die (the one that opens the door to the stinger.)
This area is right before that red switch which lowers the lift pad to the upper balcony. You must go behind the circled steelbox and use either a flashlight or a flare to reveal another pitch-black tunnel similar to the one at the start. At the end you will find something cool.
Another hidden area is right at the elevator that leads down to the area where you fight your first skaarj. While is going down there is a small dark area ahead. Contains some ammo :).
The other item that is a little hidden is another piece of armor in the room with the fans. When you are on the bridge going towards the 3 buttons to open the end, look to the right and there will be armor in the first fan.
And finally, there is a shieldbelt on the boxes near the door to the end. If you leave that room and go up the little elevator you should be able to find a way to get to it :).
Just get on the elevator and run off and then go under it to receieve a weapon.
Shoot the small steelbox right next to the superhealth onto the medium sized box.
In case you didn't know, this is the bridge which leads to the switch to open the door to the ending. If you have an ASMD; it's fastest to do a combo right above the middle of the bridge. Otherwise, use your dispersion pistol's alt fire and keep firing at the bottom of the bridge in the middle area until it breaks. A very cool secret :).
Swim behind the platform to reveal an item (medium or lower difficulty)
The first nali priest opens a secret door for you.
In case the picture wasn't enough, just go underwater and swim forward, towards the spot where the red circle is.
Take the left path, and head to very end where the switch is to activate the lift. (leads you to picture below)
I know this is a little hard to see, just shoot the wall next to the barrel in this room.
Take the right path, and a left, then stop. (leads to the picture below)
Just under the ramp on the right should be a little area to swim in. Facing towards the platform with the switch (which opens a cool room) go through the right path under water, then go through the first opening you see while swimming down. After that take your first right and swim up.
If you didn't already know, there is a dungeon at the left end of the castle (outside), just keep going all the way until you get to a bunch of rubble. Just explode it!
Okay, this is a little tricky. You see that metal ring around the pillar that rises? Well you need to get on top of that, but be quick. When you are on top of it, let it reach its highest point. Then the titan should come out. If it doesn't notice you; shoot it. Then run against the pillar and wait for it to slam the ground, sending you into the air. Try to land on the very top of the pillar.
The nali in the church opens a door for you, and there is armor behind the Nali statue in the church aswell.
This one is my personal favorite. The graveyard is right behind the church. Just go behind the circled grave and press the button, and the grave right beside it will open. Have fun exploring :)