The Hole is a secret area, built into the wreckage from the crash site of an asteroid within the Greenhouse grounds. The hideout, utilized by Ze'ev's forces is cleverly disguised as a rock formation, which can be opened up, upon placing your hand on a nearby wall, which acts as a scanner and authorizes entry to the Hole.
When you enter into the Hole, you will come down a set of stairs, that will lead down a hall, which acts as the entry point for the main office/workspace in the Hole. In the office, you will find some worktops located at different areas of the office, featuring computers and monitoring equipment, as well as access to security cameras that can see the outside of the cave. There's also a secret area of the Hole, where Marcus keeps a stasis pod, currently containing Naomi .