NERV is the organization of the "good guys" of this series. It exists under the auspices of the United Nations.
The United Nations plays a role in this series because all the money, weapons, hardware, and so on have to come from somewhere. In the series, we see military vehicles with the UN logo from time to time.
The JSSDF or the Japan Strategic Self Defense Force is basically Japan's armed forces. NERV headquarters is in Japan, and since the JSSDF are helping the UN and NERV, we often see their vehicles and personnel going about their business and doing their jobs to keep Japan safe. NERV and the JSSDF are two separate groups. NERV is a multinational effort. The JSSDF is the local Japanese military.
Project EVA is the scientific and military research and development into much of the technology you see in the series. It is basically NERV that is carrying the project out, and as such, it receives funding from (and falls under the oversight of) the UN.
Central Dogma is that place NERV headquarters that serves as a command center. It looks like the multi-level control tower of an aircraft carrier that's missing its roofs. The uppermost "deck" is where we see Misato and Ritsuko give orders to Makoto, Maya, and Aoba. Sometimes we see Gendo and Kouzou there, too.
The reason why Central Dogma has three other "decks" sticking out of it below the main command center deck is that these decks hold the Magi computers. The Magi ("Magi" is a plural word; the singular is "Magus") are three computers that handle a lot of work for NERV headquarters.
The whole Central Dogma has a huge empty space in front of it. Instead of a big computer screen, this empty space projects 3D "holograms" (for example, the lowermost is a topographic projection map thing made up of green lines). This is important to remember because sometimes the series will show scenes of a UN or a JSSDF command center with military people panicking about something. If it doesn't have these huge 3D holographic image things, then that's a clear sign that the scene is not taking place in Central Dogma.
Terminal Dogma is basically "the basement." It is located deep deep under NERV headquarters. It is important that one does not confuse Central Dogma and Terminal Dogma.
LCL is the orange-yellow liquid we see in the series.
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