2067: Isolation: Japan seals herself off from the eyes of the world in the face of unilateral international policy setting strict limits on the use of robotic technology. The island nation exists only behind a veil of seclusion. No soul shall enter. No soul shall leave. 2077: Revelation: The veil is breached. Japan is infiltrated by agents of the organization S.W.O.R.D., a fighting force operating outside of the protection of the United States and her allies. Their mission: Determine if the Japanese are developing banned robotic bio-technology, forbidden due to its threat to humankind. In the battle between machine and man, humanity stands to suffer most.

2199 AD. Yamato tried to leave behind the Large Magellanic Cloud galaxy, after receiving a “Cosmo Reverse System” at its destination, Iscandar. However, suddenly, it encounters a mysterious group at the edge of the Large Magellanic Cloud. The crew finds out that the group is called the “Gatlantis,” and that its leader is the Gutaba expeditionary force commander who calls himself “Goran Dagaamu of Thunder.” The commander demands that Yamato be handed over to him. Yamato, wanting to hurry to Earth, escapes the fray. However, Yamato is attacked by a devastating beam weapon called the “Flame Direct Attack Cannon” that can transcend space.