I've finished the game multiple times and I did not find a single secret :/ Thus, I decided to round up all the info, find the secret areas once and for all and create this guide. Hope it will help!

Just for you to know where to look, this is the level structure of the game:

• The Rift - with a mini-boss: The Tank
  
• The Rift Core - with a proper boss: The Guardian
  
• The Colony - with a mini-boss: The Shredder
  
• The Colony Core - with a proper boss: The Alpha Experiment
  
• The Foundry - with a mini-boss: SUN-MKO Prototype
  
• The Foundry Core - with a proper boss: The Sentinel
  
• The Forsaken Sector - there is no boss and it can be found in the Bunker all the way to the right

Note (this applies, I guess, for the earlier versions of the game):

• The Foundry is sometimes referred as The Armory.
  
• The Forsaken Sector is sometimes referred as The Abandoned Sector.

The portal to Trfd lies somewhere in the Colony. At some point you come to a room with two "layers". The doors of the room are in the front layer and there is a bridge at the top in the middle of the room which connects the front layer and the layer in the back. As mentioned, the bridge is in the air so you have to jump on it. It is quite obvious that the bridge is there but, I suppose, it is possible to miss it.

The portal itself is in the second layer hidden in the steel cargo boxes:











Once you go through it and talk to Trfd, you'll get the achievement.

BoredomKnight could be found in the Rift Core. You are looking for a room with a lot of pipes with prisoners or a portal in them.


The room itself is quite a big one and there is usually an opened duct (in different variations of the room):











Instead of going into the duct (which obviously you cannot) you jump on the light above at the top of the room. There, you can actually see an opening into the duct - basically from the opposite direction:











And there is a hidden portal behind the steel panel!











Once you talk to the BoredomKnight you'll get the achievement.

Furokai is in one of the rooms in the the 1st level - Rift. Once you see it, you immediately know that there is a secret area :)


You are looking for a room with a deep shaft, where at the bottom you have a big "warm" light (at least I just feel the warmth) above a door:











There is a small duct entry located at the bottom of the shaft on the right side. The portal is right behind that entry.











Once you enter the portal and talk to Furokai, you'll get the achievement.

Luc hangs on in the Foundry. You should be looking for a breakable door. The thing is, it is quite hard to recognize a breakable door (there are no wooden bars but that means nothing).

Anyway, you are looking for a room with a lot of fans in the background and a two platform bridge with a trap on the right:











The location of the door is not really obvious. Even though it is in the plain sight, it is still well hidden (good job devs!). The door is on the left side of the mentioned bridge and the portal just behind it. So behold the door:











Once you get through the portal and talk to Luc, you'll get the achievement.

You can find Warlaps in the Foundry Core. He is hiding in an elevator shaft. As you would guess, you are looking for a room where is an elevator.


In fact, the correct room has two elevators but one of the shafts (where the elevator is going up and down) is not accessible. You can actually spot the hiding place, small ventilation opening, from distance:











If you climb the ladder shown in the picture above, you'll get to a ledge with a duct entry at the top left corner. Going through the duct, you'll get to the elevator shaft. Once you jump down, the elevator will shift down a bit - the shaft is now accessible from the other side as well. Now, the opening you saw from the distance is just above your head:











It is not straight forward jump and climb, but you need to dash through it. So you might need to give it couple of attempts to time it just about right. Since you dash through the hole, you end up at the end of the pipe where you would not see the action button for the portal. Worry not, just get back a bit and there it is:











For the last time, once you get through the portal and talk to Warlaps, you'll get the achievement.