Rahxephon

RahXephon (Japanese: ラーゼフォン Hepburn: Rāzefon?) is an anime series about 17-year-old Ayato Kamina, his ability to control a mecha known as the RahXephon, and his inner journey to find a place in the world. His life as a student and artist in Tokyo is suddenly interrupted by a mysterious stalker, strange planes invading the city and strange machines fighting back. More information can be found here.

Super Robot Wars DRP
In Super Robot Wars DRP, the 'Tokyo Jupiter' was formed in the chaos that came with the Second Impact, causing a dimensional distortion that encompassed a portion of the Japanese city. As a result, modern-day Tokyo has been evacuated and sealed off from the public. Tokyo Jupiter is also known as 'Tokyo-1'. Its existence prompted the Japanese government to create the Tokyo-2 and then Tokyo-3 (with some urging from NERV).

The mysterious Bahbem Foundation has worked with N.U.N.S. to create the defense research agency T.E.R.R.A in order to find ways to breach the Tokyo Jupiter. This agency's domain has expanded to also handle the interdimensional threat of the Mulians and the Dolems, similar to NERV's own focus on the mysterious Angels. They operate from the island base of Nirai Kanai.