One year after Philip's merging with the true Gaia Memory, after leaving a pet shop upon giving the third degree to one of its workers for not having cat food he needed, Shotaro is followed by a young boy named Akira Aoyama who needs help finding his sister Yui who has gone missing for three days. Taking the case, and Akira with him, Shotaro goes to Watcherman and Queen & Elizabeth, learning that Yui was last seen with a gang calling themselves "EXE" who are buying Gaia Memories.