Life for Ayato Kamina seems normal enough, but when wars hits close to home, the life he once knew changes forever.

With the RahXephon awakens, the tide of war seems as if it is about to change, The RahXephon, under the control of Ayato, easily eliminates the invading Dolem.

Ayato has discovered the shocking truth: his mother has blue blood. The RahXephon destroys another Dolem and creates a passage from Tokyo to the outside.

Having left the "safety" of Tokyo and now living on the outside, Ayato and Haruka are picked up by TERRA, the military group that she is a member of.

Having taken care of the Dolem threat, Ayato has proven that he can be trusted, and is taken to a new home.

The media has somehow picked up on the knowledge that TERRA has a new weapon in their fight against the Mu, but they keep running into a brick wall of plausible denial.