In 2199, the crew of the space battleship Yamato set out on a journey to the planet Iskandar to acquire a device that can heal the war-ravaged Earth. In 2199, five years after the Gamilas launch attacks on Earth, the planet has been ravaged by the aliens' radiation bombs and the remnants of humanity have moved underground. One day, former pilot Susumu Kodai discovers a message capsule sent from the planet Iskandar that tells of a device that can remove the radiation from the Earth's surface. The United Nations of Space Administration rebuilds the battleship Yamato, with a new type of propulsion system - the Wave Motion Engine. This enables her to make the long voyage to Iskandar and back in hopes of saving the Earth. Within 73 days, the radiation will drive the rest of humanity to extinction and the Gamilas will inhabit the Earth.

Bekushiru: 2077 Nihon sakoku - Japan, 2077: A female agent named Vexille is dispatched to Tokyo to investigate whether Japanese are developing robotic technology, which has been banned by the U.N. due to its potential threat to humankind.