A man wakes up disoriented, deep inside an underground cave. Suffering amnesia, he has no recollection of who he is, or how he got there. A dead man lies next to him. As he stumbles around in the limited light, he comes upon a dilapidated area with damaged pieces of technology all around him. A registration plays, explaining the place is a sort of processing network called Eden Log, whose workers are all immigrants promised citizenship in the society above ground. The workers are apparently harvesting the sap of a gigantic plant whose roots and vines are now everywhere in the underground complex, which appears abandoned.
While trying to reach the surface, the man comes upon a bearded stranger pinned against the wall by the protruding vines that are slowly taking over his body. The stranger, in great pain and sounding deranged, tells the man he's the creator of that entire system, and then warns him about an unseen menace. A growling noise approaches and the man loses consciousness.
Upon waking up, the man keeps going up, passing throughout areas increasingly better-lit. He retrieves more recordings, revealing that one of the network technicians refused to give access to security personnel. It becomes clear that some kind of revolt was started by the workers over the conditions in the network. As a result, the corporate overlords ordered the security forces to forcibly take control of the network levels and seal the area.
The man climbs up to Level -3, where he overhears some security personnel talk about their orders to capture "the architect". They also have what looks like a mutated human chained up, and it's revealed that a significant amount of the worker population have changed into mutants.
On Level -2, the man ends up in a small laboratory, which is suddenly surrounded by mutants. A figure in a protective suit uses a bright light and loud noise to scare the mutants away, then knocks the man out and restrains it, fearing he's infected as well. The figure, being one of Eden Log's botanists, explains the goal of the entire structure is to generate power form the sap of the living plant at the center of the network. However, at some point the plant has started to react, triggering the mutation. The botanist conducts a test on the man, connecting briefly with the plant, but surprisingly, the man seems to be able to reverse the corruption process, causing the seemingly sterile plant to sprout and become lush with growth.
Shortly after, the mutants resume their assault on the botanist's lab, and the botanist flees, leaving the man behind. After escaping a mutant, the man catches up with the botanist, who's revealed to be a woman. The two are now on an elevator, and during their ascension, the man is suddenly overwhelmed by a sexual urge, that quickly degenerates to the point that he brutally rapes the botanist. She's traumatized, but the man seems to have lost control of himself only temporarily, due to the peculiar sort of mutation he's experiencing. He realizes he had killed the architect as well, before blacking out.
The botanist agrees to follow the man, despite being still wary of him. Together, the two traverse several tunnels, and eventually stumble upon the location of a technician who merged with the plant to stop the mutation. Fending off the mutants, they reach the sap collector at Level -1. The botanist sees white cubes with human workers inside, and realizes that's where the infected are stored, not to be cured but to be exploited for energy themselves: the dangerous "secret" the corporate woman from the registrations had alluded to.
The botanist begins convulsing and realizes she had been infected by the man when he raped her. She tosses him a final data chip with recordings, then runs away, back into the tunnels.
Proceeding upward, the man emerges in a chamber that he seems to recognize. He sneaks into a surveillance room and begins watching the videos and piecing all the information together, finally rediscovering his own identity: his name is Tolbiac and is the commander of the security tasked to quell the rebellion. After being infected, he killed in a rage the guard who was with him, losing his memory afterwards. The computer system now confirms his mission was successful, having killed the architect, stopped the revolt, and recovered all the data from the technicians. A group of guards enter the room and, upon recognizing their chief, stand by waiting for orders.
On the surface, Tolbiac is saluted by Eden Log's corporate people for protecting the company's secrets as he stands in front of an animated board depicting the full process of the power harvesting procedure: the immigrant workers are purposely sent to the lowest levels, given sap to energize them, then work until they are depleted or dead as their energy is harvested to power the city above; this society's way to "integrate" the immigrant populations.
Tolbiac decides to break this cycle, as he walks into the tree's main chamber and plugs himself in, causing the plant to undergo explosive growth, which destroys the power plant and causes a full blackout in the surrounding city. The tree's growth overruns the city, while a single tear falls down from Tolbiac's eye.
Who salutes Tolbiac, at least on the surface?
Eden Log's corporate people