As a child in 1999, he witnessed the fall of the Macross and the war that followed. During these so called U.N. Wars his family was killed in front of his eyes, a memory that would haunt him for the rest of his life. Later he would join the U.N. as a skilled fighter pilot flying the F-14. During a mission he is shot down by the transformable SV-51 and lands in Mayan Island. He would later fly the new VF-0 variable fighter under the tutelage of Roy Focker.
Due to his horrifying experiences as a young child, Shin grew up to be a quiet and untrusting person. Aside from his rear-seat radar intercept officer, Edgar La Salle, he has very few friends, and is slow to trust. His interactions with the infectiously cheerful Mao Nome and her more reserved sister Sara help him open up, especially his growing attraction to the somber and mysterious Sara.
During the final episode, the extraterrestrial object known as Bird Human (or Bird People) 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 realize that it is Shin instead of an evil spirit (called a "Kadun" by the Mayans). The UN-Forces, however, see the Bird Human as an uncontrollable liability and launch several Nuclear Missiles at the Bird Human. Sara then 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, allowing the Valkyrie fighter to fly, with blue particles trailing the wings and tail section of the plane. Finally an amazed Mao Nome watches Shin Kudo & his fighter ascending into space in the same way that The Bird Human did, supposedly to be with Sara.
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