TOKYO-3

Tokyo-3 is where most of Evangelion takes place,as NERV is located inside of it and many of the characters live there.

A fun fact about Tokyo-3 is that the buildings can actually retract into the ground when there is an attack.

Some buildings also contain weapons for the EVAs.

The reason why it was built was to intercept all angel attacks in japan by creating a fake capital city

.It is also said that Tokyo-3 was indeed meant to replace Tokyo-2 as the capital of japan, but that may just be to cover the construction costs

TOKYO-2

Tokyo-2 is the real capital city of japan in Evangelion,

as the actual Tokyo had been destroyed by a bomb during the Second Impact.

The government resides in Tokyo-2

since it would obviously be too dangerous to be based in Tokyo-3, where there are basically daily angel attacks.

Other than that, it is barely seen in nge.

everything honestly gets so confusing past this point, good luck

NERV is located at the bottom of the GeoFront,and has so many

different parts and divisions that it's very confusing to explain what is inside of NERV.

NERV is essentially a black pyramid in the geofront,

which also has an inverted pyramid connected to it that contains the base's water reserves.

All personell/visitors of NERV can take a range of train and car services that go through the Geofront and into NERV.

NERV also has tons of different floors and subsections that contain things like hospitals, canteens, changing rooms, ect.

(we actually don't have any offical maps of NERV headquarters, so i'm using the map that Misato used in episode 1 as the image)

This is the deepest and most secret level in the NERV headquarters, where only those who have the highest level of clearance

(like gendo) can access.

Within Terminal Dogma there is the LCL production plant, where they keep Lilith crucified with the spear of longinus.

The graveyard for prototype EVAs and the cloning facilities are also in Terminal Dogma.

This is where NERV's primary command centre is located, and where the Magi supercomputers are based.

(There is also a backup command centre located several layers down

(A geofront is actually the term used to describe a subterranean cavity. wow.)

However, the GeoFront in Evangelion is not a natural cavity, but instead where the egg that carries Lilith had created a giant hole

After discovering this cavity, both NERV and Tokyo-3 were constructed inside it

(NERV was built directly inside the cavity, while Tokyo-3 was built ontop of it, so that the buildings can be hidden during battle).