Secret Places (5)
In the first main room (dark until lights are activated), press on the suspicious looking door-like texture in the wall beside the computers. There is a second door behind it. The secrets are behind the second door. For some reason, the player will be credited for two secret places even though it looks like one.
Jump into the EDF logo.
In the first flashing room, look to the left of the computers. Press on the walls until a door opens. It's quite easy to find.
In the second flashing room, open the closet-like structure. The secret is in the dark corner.
Unofficial Secret Places
There is another suspicious door-like texture in the first main room. It contains nightvision goggles.
In the final area (covered with slime), use a jetpack to locate the gun turret crevice. At the back is a bright texture (as seen in the image). Open it to find a hidden area.
Secret Messages
"1138". Can be seen through the security camera in the first secret place. It can also be spotted in tiny print beneath the EDF logo.