A.D. 2008. Eight years into the Unification War, U.N. Military and Anti-Unification Alliance forces converge on the remote Mayan Island to attain an alien relic. U.N. pilot Shin Kudo gets shot down in his F-14 and washes ashore on the island where he meets the priestess, Sara, and her sister, Mao.

Shin is rescued by Sara and Mao on Mayan Island and stays with the sisters. A fierce battle between a U.N. Military and an Anti-Unification Variable Fighter cuts through the sky. When the U.N.'s new VF-0 unit crashes right in front of him, Shin hops into the cockpit without a second thought.

Mao takes Shin free diving to see her treasure hidden deep within the sea. Meanwhile, the Anti-Unification Alliance and U.N. Military engage in a fierce sea battle for possession of the Bird Human. The fighting quickly intensifies, engulfing the once peaceful Mayan Island in violence.

Deep in the jungle, Nora holds Shin, Sara, and Aries captive in the Anti-Unification's hideout. There, they meet anthropologist Dr. Hasford. Meanwhile, Focker engages his rival, D.D. Ivanov, in another fierce battle in the skies above Mayan Island.

The fierce battle over the Bird Human activates the Protoculture relic, Bird Human. When Shin learns Sara is inside the Bird Human, he rushes to rescue her in his VF-0 as Focker fends off his greatest rival, D.D. Ivanov.