A quick guide for beating the Beta Branch Secret Level [Spoilers]

[Taberone]

Recommended loadout: Nailer (Has Armor Piercing, enemies use it so you can get ammo) + Bolt ACR (Useful and overpowered in general, lure enemies into the radiation clouds so they die)

Recommended augmentations: None because you can't use any, you'll lose all your augmentations when the level starts due to a mysterious, malignant force

Recommended status effects: Anything but Hope Eradicated (Hope Eradicated makes it harder to see and makes the fog worse, reducing effective draw distance and making it easier to get killed by enemy snipers. Hope Eradicated also adds more enemies in locations that will kill you unless you've already died to them at least once.)

Strategy: Find the out-of-place book in the library and the floor will sink after you activate it. Make your way into the cave and use the Bolt ACR on the Giant Fleshrat. Then, fire the ACR upwards into the ceiling where the cave opens up and kill the Rocket Launcher enemy through the ceiling, otherwise he will instakill you from behind.

Take out the Fleshmen with those giant heads and the Nailer Guards, and then take out the sniper in the tower to the right before he headshots you. Beware, for the Fleshmen drop Fleshrats on death if they explode into gibs.

Find the house outside the cave, then go to the bottom left door and use the Nailer to kill the unique Armored Zombie with headshots. Find a giant pit and jump into the second cave, using the slopes to cancel your fall damage. You'll be surrounded by Giant Fleshrats. Avoid them and go into the part of the second cave that goes down to the bottom by climbing the ladder down.

Once you climb the ladder down, make a run for it. There's fleshrats at the bottom of the ladder, armored fleshrats and fleshpigs outside, and Rockmen everywhere who are immune to everything that is not Armor Piercing. Don't look back, just keep running forward and bunny-hopping. Make your way to that giant orange orb and you'll unlock Ending #3. I'm not sure if this is the True Secret Ending, but it sure feels like it for now.

[Omni]

So, there's nothing at the end of other way of the house outiside the cave, behind the sniper? I went all the way down there, killed unique enemy, ended up in rooms with huge barrels, but I dunno if there's any way to progress there

[Taberone]

Minor correction: Don't go up the stairs when you reach the house outside the cave, go to the bottom-left door and enter the corridor with the armored zombies. Proceed through the corridor until you find a circular hole that drops you into a cave full of giant fleshrats, then run past them until you find a ladder that takes you to the bottom.

Once you get to the bottom, just run for it and keep bunny-hopping your way to the orange portal.

[Samz]

As someone who could never survive the slopes, there's a hidden door in the bit you fall in the second floor of the house that allows you to keep moving on and not get killed by the stone golems.

Also on the roof of the house (using the stairs) you can kill the "Ambassador" who will stay dead and drop a transactional rifle.