Central Dogma is the codename for the primary subsection of the Nerv Headquarters building complex. It is located beneath the Headquarters' black pyramid, and is accessible via. a main shaft within the building itself.
Central Dogma, along with the rest of Nerv HQ, was constructed by Gehirn shortly following the Second Impact, inside the Black Moon in Hakone, Japan. At the time of the Headquarters' construction, many scientific experiments were underway in Central Dogma, including Naoko Akagi's development of the Magi System, and Naoko's collaboration with Gendo and Yui Ikari on Project E. Central Dogma switched hands when Seele dissolved Gehirn and created Special Agency Nerv to fulfil the goals of the Evangelions and to advance Seele's own agenda. Most, if not all of the Necessary facilities for the Evangelions were built at this time, suggesting Central Dogma's intended use was that which it was used for in the series. Although neither Yui nor Naoko lived to be part of Nerv, their scientific research was continued and eventually used in Central Dogma following the transfer. In it's early stages, Central Dogma was composed mainly of dimly-lit hallways connecting important rooms, with wires running along the floors and walls. Parts of the facility were never finished, likely due to budgetary restrictions.
Nerv's Command Center is located inside Central Dogma, where operations involving the Evangelion units are coordinated. The Command Center also houses the original three Magi supercomputers developed by Naoko Akagi.
The other Nerv Facilities housed within Central Dogma include:
- The Backup Command Center, located several levels below the primary one. Used following the battle against Zeruel, the Magi are transported here as well.
- The Evangelion Cages, where the Evas are kept and maintained, when they are not deployed.
- The Pribnow Box, containing the Simulation Bodies.
- The Artificial Evolution Laboratory; the alleged location of Rei Ayanami's birth.
- The Dummy Plug Plant, used to produce soulless clones of Rei Ayanami for use as spare parts, and as the cores of the Dummy Plug. It is located deep within the "central area" of Central Dogma.
- The Training Facility, where Shinji Ikari is first taught how to operate his Eva.
- A Facility for testing the Synchronization Ratio of pilots.
Terminal Dogma is located at the lowest level of Central Dogma. It is very far down from the rest of Central Dogma, accessible only by Elevator with high-level security clearance. Terminal Dogma is the location of the "LCL Plant" -- the place where LCL is "created". It is actually the resting place of Lilith, crucified on a red cross, bleeding LCL.
Central Dogma fulfils the same roles almost identically in Evangelion 1.0 and 2.0, although it's history has not yet been disclosed. After Near Third Impact in Evangelion 2.0, Central Dogma (along with the rest of "Old Nerv HQ") is almost completely destroyed. In Evangelion 3.0 the extent of the damage is known: most all of the facilities are damaged beyond repair and defunct, and many of the rooms are littered with Failures of Infinity. Lilith's severed head can be seen in the Command Center, and Terminal Dogma has been altered drastically since N3I. The Eva Cages are exposed to the sky, and coated in Red Dust. The base of operations for Nerv appears to have relocated to the upside-down pyramid in the sky above The Geofront, although the extent of those operations and the details of the New Headquarters are still a mystery.
- The origin of the name is attributed to the Central Dogma of molecular biology, which deals with the transfer of DNA information within a cell: DNA is transcribed into RNA, which is in turn translated (at ribosomes) into amino acid sequences that construct proteins, which are the main structural constituent of living cells. Put more simply, "DNA to RNA to Proteins". 
- The Main Shaft is explicitly mentioned in Episode 19, and is the method of which the Angel Zeruel invades Central Dogma and the Headquarters.
- No time frame for it's construction is given, but based on the level of completion of Nerv HQ when Fuyutsuki visits in in 2003 (Episode 24), the Headquarters likely began construction in 2001/2002.
- This detail may only be relevant in the Rebuild Movies, as it is never explicitly mentioned in the original series, although the same budgetary concerns are eluded to.
- It is unclear whether Terminal Dogma is considered part of Central Dogma or is simply below it, however the name connection suggests the former.
- Supposedly 2008 meters below, making it roughly 3 km below the surface. It's unsure whether Terminal Dogma is at the centre of the Black Moon or not.
- Only Gendo, Fuyutsuki, and Ritsuko are known to have the security clearance to access Terminal Dogma, however they are not the only ones who know of it and who visit it in the series.