Source: The End of Evangelion : Glossary contained within The End of Evangelion - Theatrical Program.
The new capital of Japan built in the former Nagano Prefecture to replace the old Tokyo. Construction started in 2001, and the city acquired all the necessary functions for a capital by 2003. According to the Second Capital Relocation Plan approved in 2005, it was planned that the capital would be moved to Tokyo-3, which was still under construction at that time. Incidentally, old Tokyo was obliterated by Second Impact and a new type of bomb dropped just one week thereafter. Thus, the construction of New Tokyo-2 was decided by the Provisional Government of Japan. When Makoto Hyuuga mentions "Tokyo-2" in episode 25' "Air", he is referring to this New Tokyo-2 as well as the government of Japan which is located there.