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Tokyo-1 (the original Tokyo) is now a partially submerged ruin seen in the series. It was destroyed on September 20, 2000, seven days after Second Impact, when a nuclear bomb was dropped on it during the wars which broke out as a result of post-Second Impact tension. The destruction of Tokyo-1 resulted in the death of half a million people. An official document on the Second Impact is shown in the series for a brief moment. The Japanese Prime Minister also states in The End of Evangelion that he wants Tokyo-3 to be so utterly destroyed and made completely uninhabitable that "no one can touch it for the next 20 years... like old Tokyo."
Tokyo-2 is the capital of Japan, and was where the Japanese government relocated after Tokyo (Tokyo-1) was nuked in the chaos following Second Impact. Tokyo-2 was created in the location of today's Matsumoto City in Nagano prefecture. Construction began in 2001 and by early 2003 it had become the functional new capital city.
New Tokyo-3 City (第３新東京市, "Dai-san shin Tōkyō-shi"), commonly known as Tokyo-3, is located above the GeoFront, with buildings of that can retract into the ground for safety, and other buildings that contain the launch ports and weapons caches for the Evas. It is projected to replace Tokyo-2 as capital of Japan, but was designed to intercept all incoming Angels to Japan. The city is defended by numerous missile stations around it. It was built in the location of pre-Impact Hakone, approximately 80 kilometers southwest of Tokyo-1. In Episode 01, Shinji is picked up in the neighboring city of Atami, 25 kilometers away.
Tokyo-3 was heavily damaged by the attack of the Angel Zeruel, though repairs on NERV HQ and much of the city were worked on later. However, soon after Rei was forced to self-destruct Unit-00 to destroy the Angel Armisael, a large swath of the city was destroyed. During the attack by JSSDF forces, the Invaders systematically take out sensor posts and the missile stations and proceeding to invade the Geofront Base below while a N² Bomb exploded in the city destroying it entirely and leaving the Geofront open to the sky, though NERV HQ (located deep beneath the area of the blast's effect) survived the explosion.
Rebuild of Evangelion
In Evangelion: 2.0 You Can (Not) Advance, Evangelion Unit-00 (Rebuild) and Evangelion Unit-02 (Rebuild) coordinated a N² missile attack on the Tenth Angel while inside the GeoFront, the detonation of the N² missile destroyed most of Tokyo-3 and left the Geofront exposed to the open air. Mark.06 used this opening to descend into the GeoFront and stop Evangelion Unit-01 (Rebuild) from initiating Third Impact at the conclusion of the movie.
In Evangelion 3.0: You Can (Not) Redo, Tokyo-3 can be seen when Kaworu shows the results of Near Third Impact to Shinji; all of life is destroyed, covered with a reddish substance and sprinkled with bits of beings resembling Evangelion Unit-01. The atmosphere of the city seems toxic to humans as Shinji is forced, unlike Kaworu, to wear a suit to visit it.