As the project itself was designed to as an alternate-reality counterpart to Doom itself, this episode shares the original episode's name, theme, and story, placing the player back in the familiar world of the UAC base on Phobos. This leads to a blue armour and rocket launcher. In the slime room directly after the first secret there is a secret door in the slime pit where the wall is a different colour. In this room behind the barrels is a secret door with some shotgun ammo.
Knee-Deep in the Dead, named after its counterpart episode in Doom, is the first episode of Doom the Way id Did. Early in the level you will walk up some stairs.