As a child in 1999, he witnesses the fall of the Macross and the following U.N. Wars. His family is killed before his eyes, a memory that would haunt him and turn him into a quiet and mistrusting person. He joins the U.N. Spacy as an F-14 fighter pilot. During a mission he is shot down by the anti-U.N.'s transformable SV-51 and lands in Mayan Island. He later flies the VF-0 Phoenix variable fighter under the tutelage of Roy Focker. Aside from his rear-seat radar intercept officer, Edgar La Salle, he has few friends and is slow to trust. His interactions with the cheerful Mao Nome and his growing attraction to her more reserved sister, Sara, help him open up.
During the final episode, the extraterrestrial object known as Bird Human by the Mayan people awakens, assimilating Sara into the cockpit located at its head. He manages to break through the Bird Human's attacks and makes Sara realise that it is Shin instead of an evil spirit (called a "Kadun" by the Mayans). The UN forces, however, see the Bird Human as a liability and launch reaction weapons at it. Sara sacrifices herself to save Shin and the rest of the Mayan Island which would have been destroyed by the nuclear fallout. The Bird Human is critically damaged from the blasts and shoots off into space incredibly fast in what appears to be a space fold. Shin's VF-0 suffers engine damage from the blasts and plunges towards the ocean. He is seemingly saved from certain death by Sara. Finally, an amazed Mao Nome watches Shin and his damaged fighter ascending into space in the same way that the Bird Human.
Shin's experiences were later portrayed in a movie called The Bird Human. Alto Saotome, a former kabuki actor, agreed to double for the main actor portraying Shin during an underwater scene. (F: "Legend of Zero")