In 2199, five years after the Gamilons began an invasion of Earth, the planet has been ravaged by the aliens' bombs. The remnants of humanity have fled underground to escape the irradiated surface. One day, former pilot Susumu Kodai discovers a capsule sent from the planet Iscandar that tells of a device that can remove the radiation from the Earth's surface. The Earth Defense Force rebuilds the battleship Yamato with a new type of propulsion system to make the 148,000 light year trip to Iscandar in hopes of saving the Earth. Within one year, the radiation will drive the rest of humanity to extinction.

Two leading computer scientists work toward their goal of Technological Singularity, as a radical anti-technology organization fights to prevent them from creating a world where computers can transcend the abilities of the human brain.

When the crew of the Enterprise is called back home, they find an unstoppable force of terror from within their own organization has detonated the fleet and everything it stands for, leaving our world in a state of crisis. With a personal score to settle, Captain Kirk leads a manhunt to a war-zone world to capture a one man weapon of mass destruction. As our heroes are propelled into an epic chess game of life and death, love will be challenged, friendships will be torn apart, and sacrifices must be made for the only family Kirk has left: his crew.