Having come off second-best in his first battle with an Anti Alliance transforming fighter, Shin awakes to find himself stranded on an island, Mayan. Stuck with them while his wounds heal & while he tries to find a way to signal his base, he strikes up a friendship with island girl Mao, and an understanding of sorts with Mao's older sister, Sara.

The Alliance have developed their own transforming fighter, the VF-0 (or 'Zero'). It first sees action in the skies above Mayan, placing the lives of Mao & the other islanders at risk but giving Shin his opportunity to return.

Shin discovers that Sara and Mao have strange abilities connected to the island. Tension between Sara and Aries intensifies when Sara's mentor was the same professor that drew blood from her at a younger age. Meanwhile, Mao brings Shin into the ocean to show him the island's "secret treasure" - a large fragment of the ancient relic known as "AFOS." There, Shin learns more about adapting to different environments by observing a school of flying fish and a flock of birds that also swim. But Mayan and the ocean surrounding it once again become a war zone when anti-U.N. forces attack the Asuka II fleet and the island in hopes of taking away the heavily-guarded AFOS. Shin and Edgar - aboard their VF-0D - must protect the AFOS fragment discovered by Mao from the invading forces.

After crash-landing, Shin finds a priestess in the Mayan jungle. Although they both are captured and tortured, they manage to escape but they are relentlessly chased by their enemies.

In the South Pacific, two military forces prepare to fight a nuclear war. In desperation, Shin and Sara decide to sacrifice themselves . . . in order to protect the Mayan people.