E1, M5: Phobos Lab
This level has a whopping 9 secrets to get 100% secret completion.
Secret 1
After crossing the slime pool, you will come to a set of stairs. In the room they lead to, there is a secret door with shotgun shells inside behind the barrels.
Secret 2
There is a secret door in the slime pit directly after the first secret area. Jump off the walkway and into the slime to reach a brownish, oddly-colored wall. This secret area contains a blue piece of armor and a rocket launcher.
Secret 3
On the far side of the yellow key door room, you will find a little alcove with a health kit in it. Behind the health kit is a secret door that leads to a biohazard suit and secret areas 4 and 5.
Secret 4
The tiny space in secret 3 has another hidden door to the left that reveals a chainsaw.
Secret 5
After you pick up the chainsaw in secret 4, push the walls to discover yet another secret door. This one takes you outside for a soulsphere.
Secret 6
There are two ways to get to this secret area, you will find the alternate way as part of secret 9.
Still within the yellow key door area, there are platforms that lower as you walk by them. If you stand on one of them and ride it all the way up, there is a secret door that opens to reveal a room containing a blursphere.
Secret 7
In the weirdly lit computer room that has a switch that opens a wall, check the wall on the other side of the column to the right of the switch to uncover a secret door that hides an automap and chain gun.
Secret 8
In the locked blue key door is a very dark room. If you turn left immediately on entry to this room, you will discover a small tunnel with a pair of light goggles at the end.
Secret 9
Now that the blue key room is lit up, it is easy to explore and locate a section of green wall. This is a secret door, which leads to the same room with the blursphere that can be found in secret 6.