In the year 1999 a huge extraterrestrial battleship crash-landed on Earth, bringing the human race in contact with very advanced technology. Human short-sightedness and the greed to be the only one to possess this technology led to the war between the UN and the Anti-UN Eight years have passed since then, killing so many veteran pilots that even boys in their teens had to be recruited to fight the war.

Kudou Shin, a young UN F-14 pilot is shot down by an unknown enemy fighter plane during a sortie and crash-lands on a solitary island.

Coincidentally, an unusual energy surge is detected on this island. Both sides of the conflict suspect the surge originated from remnants of the Proto-culture's advanced technology, left behind by extraterrestrial beings in ancient times. As it turns out this technological legacy is very similar to the recovered fallen extraterrestrial battleship that crashed eight years ago.

Now, both the UN and the Anti-UN struggle to be the first to recover the technology of extraterrestrial origin by invading the island... bringing death and destruction to the peaceful islanders.

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Sequel: Choujikuu Yousai Macross