Originally intended to be a replacement third capital of Japan (after Tokyo-2, formerly Nagano City), the city was built on the location of the pre-Second Impact towns of Ubako and Sengokuhara within Hakone, in Kanagawa prefecture, on the northern shore of Lake Ashinoko.
However, its true purpose is to coordinate the interception of Angels heading for Japan, covertly using Lilith as a means of attracting their attention.
Tokyo-3 spans roughly 1.5 km in length from one end of the city to the other, arranged in 5 "blocks," with each "block" section being 300 meters long. It is apparently composed of a "central block" and seven "districts."
Local government comprises of a city mayor and a council, all elected to office by popular vote, but most city operations and decision-making functions are made by Nerv's MAGI supercomputer.
Below the city lies the GeoFront, a massive semi-spherical cavernous formation which also houses Nerv Headquarters.
As a Fortress City
Prior to any Angel attack, residents are immediately directed to emergency civil defense shelters located around the city perimeter; each shelter is fortified with thick ferro-concrete walls and large enough to keep thousands of anxious residents protected and supplied with ample amounts of food, water, sanitation, ventilation and heating.
Nerv's Evangelion Units are also launched from under the city, using access gates disguised as buildings, to fight the Angels. Furthermore, Evangelion support facilities, including power sockets and cords, and weapons caches are located throughout the city at strategic locations, all disguised as buildings.
Tokyo-3 was damaged for the first time (to unknown but probably limited extent) by 3rd and 4th Angels Sachiel and Shamshel, and heavily damaged by the attack of the 14th Angel Zeruel, though extensive repairs were subsequently made.
However, not long after those incidents, in order to defeat the 16th Angel Armisael, Rei self-destructed Eva-00, resulting in a massive explosion which destroyed a large central portion of the city, creating a new artificial lake in the blast crater, and weakening the protective armor plating between the surface and the Geofront (although the section containing MIsato's and Rei's apartments survived).
During The End of Evangelion, Seele working through the UN, orders the JSSDF to assault the city, culminating in an all out assault with all remaining N² Bombs, destroying the entire city, and leaving the GeoFront below, including Nerv HQ, completely exposed.
However, once Third Impact came into being, with the combined Rei/Adam/Lilith hyper-being raising the Geofront and the entirety of the Black Moon from out of the Earth, whatever was left of the city and the surrounding countryside was obliterated, leaving nothing but a giant crater in its place.
- It is said that Shinji lives in "the old part of town."
- Misato's "Comfort 17" apartment is located at the northern city district, nearby Route 138 and also closer to Tokyo-3 City First Junior High School.
- How they are stowed and stored in this way is considered an engineering feat in itself, as these buildings weigh hundreds of thousands of tons of ferro-concrete, but they are shown positioned down into the Geo-front, with only powerful hydraulic actuation systems and locks securing them in place.