Site-Zero is the name given to the organic structure where the T'lan are first discovered. It is of unknown origins with the Carter Science Center being built directly above it in order to conduct further research. Described by scientists as a "casket" it is determined through carbon-dating to be 400 million years old. It is hypothesized that the plant life, predominantly ferns, was either brought to Site-Zero from the Earth or, conversely, spread to the Earth from Site-Zero.
Site-Zero is divided into three main areas: Sanctuary, Silo, and Core.
The entrance to Site-Zero is Sanctuary. Sanctuary consists of a fully enclosed ecosystem including plants, animals, water, and an artificial sun. While no creatures are seen in game (aside from the parasitic-type creatures and T'lan), birds (predominantly seagulls) can be heard in the background. Also present throughout Sanctuary (and all of Site-Zero for that matter) are glowing lights of energy which hover around. Within Sanctuary is a large bipedal fossil (described in game as a "mummy"). Its origin is unknown, an the research conducted on it is both vague and incomplete. The far side of Sanctuary consists of a large "Elevator Tower" leading to Silo.
Silo is a large bio-organic factory which doubles as the barracks for the T'lan Army. It is the primary staging area for the T'lan and thousands, if not millions, of T'lan soldiers are being created and moved around this facility regularly. The upper level of Silo functions as a large "launch-pad" for the rockets being constructed underneath. The countermeasures put in place by the military are the only thing preventing these rockets from launching. A lift platform leads from Silo to Core.
Core is the very center of Site-Zero. This is where Nexus resides. From here, Nexus commands the T'lan Army and maintains control over Site-Zero. With the military's countermeasures in place, many of Nexus' commands are blocked and overall control of his army is prevented. Despite this, he still maintains control over many T'lan, including Solus. Nexus is still able to maintain basic control over Site-Zero and, as such, the ecosystem of Sanctuary and the overall structure of Site-Zero remains intact.
Two types of gates exist throughout Site-Zero: Solid Gates which can be manipulated by the T'lan (presumably through control by Nexus) and Webbed Gates which can be manipulated through a general displacement of energy. Webbed Gates appear as large red-orange walls of energy. There are two large Webbed Gates: one within Terminus 4, and another at the entrance to Site-Zero. These large gates are opened by the military using a specialized LASER (similar to that of the experimental Anti-T'lan Laser). At least two smaller Webbed Gates are opened by Cole via touch (likely possible due to the presence of T'langen). Many Solid Gates exist throughout Site-Zero which function primarily as air-locks. While in a green-state, gases cannot pass through. This ensures that Site-Zero's ecosystem remains compartmentalized and self-contained. While in a red-state, solid objects are unable to pass through as well. This is done to prevent intrusion. This red-state often transitions to green upon the removal of all nearby T'lan. While these solid gates are documented as being unable to be opened, even by the military, it is later seen that De Luca's men were able to open at least one such gate through the use of the specialized LASER [bears further investigation].
Site-Zero appears to be somewhat unstable though the frequent (regular?) cause of tremors is often written off as normal tectonic activity. It is later revealed that these tremors are actually caused by the gearing-up of the impending invasion (notably, the production and staging of T'lan rockets) and likely Nexus' struggle for control.
Site-Zero's overall appearance is that of an organic-construct. Much of the structure seems to have been "grown" rather than built. It's likely that the structure itself is that of an alien "seed" which "grows" until it reaches a suitable capacity to "bloom." At this point, it launches its spore-like vessels across the globe which in turn deploy T'lan soldiers for conquest. Conceptually, it could be inferred that once a planet has been conquered, additional "seeds" may be produced for galactic dispersal on other, suitable host-planets. Site-Zero as a whole may in fact simply be an alien terraformer.