- As the Milky Way and another galaxy pass through each other, the Yamato discovers that Galman-Gamilus has been devastated, with no sign of Desslar. Later, as planet Denguil is destroyed by a flood from the wandering planet Aquarius, they rescue the Denguil Emperor's son. The Yamato is then attacked and its crew totally incapacitated by Hyper Radiation torpedoes launched by Lugarl, the Emperor's other son. The Yamato however returns to Earth on its own. On the city-satellite Uruku, the Emperor learns of Denguil’s fate. Since Denguil is now uninhabitable, the Denguil Emperor decides to warp Aquarius to Earth, flood it, and then migrate there.
- The advance Denguil forces destroy all of Earth's ships, leaving only the Yamato. Kodai resigns as captain, so Commander Todo installs the now-recovered Captain Okita back as commander of the Yamato and the Yamato intercepts Lugarl's forces at Pluto. The Cosmo Tigers take off and Okita orders the fighters to destroy the Hyper Radiation bombers first. A couple Hyper radiation torpedoes get through but the Yamato's escort destroyers move in between and sacrifice themelves. Lugarl recalls his forces briefly, but it is only a trick and they immediately return and mercilessly slaughter the aid workers. Kodai and Yuki take off in the Cosmo Zero and locate the Denguil main carrier, after which Okita destroys it with long range guns. The Yamato lands on Aquarius, where the spirit of Aquarius appears and tells them that the Denguils are ancient relatives of Earth humans.
- As the Yamato leaves Aquarius, Lugarl attacks again with more radiation missiles. However by this time Sanada has developed a device which creates a barrier shield against the missiles. Lugarl resorts to beam weapons which outmatch the Yamato's main guns, so Okita orders the Wave Motion Gun to be used. Lugarl's fleet is destroyed and he attempts to return to Uruku but his father (the Emperor) activates a neutrino beam screen which destroys him. The Yamato narrowly misses impacting the screen and veers off, but the Emperor fires a neutrino beam at the Yamato which envelopes it. Fortunately, leaking Wave Motion energy shields the Yamato from the effects of the neutrino beam, giving Okita the idea to use the leaking Wave Motion energy as a buffer to penetrate the neutrino beam screen. The Yamato crash lands on Uruku, while the Emperor attempts to warp Aquarius to Earth.
- A ground battle ensues and Shima is seriously injured. Nonetheless Kodai orders him to raise the ship so that the Cosmo Tigers can launch from the 3rd Bridge. The Yamato is stuck, but Shima uses the rocket anchor to help drag the Yamato out of the ground, and the Cosmo Tigers are able to launch. The main warp transmitter is destroyed, but the Emperor activates a backup at the Uruku shrine. Kodai confronts the Emperor and attempts to broker a peace, but the Emperor tries to shoot him. The Denguil boy, the Emperor's son, gets in the line of fire and his killed. The Emperor completes warping Aquarius towards Earth and sets Uruku to self-destruct. He and his subjects escape in their ships. The Yamato attempts to take off but doesn't have enough energy remaining. Okita tells Shima to fire the reverse rockets into the ground, further weakening the structure of the satellite, and the Yamato escapes by sinking through the bottom of the Uruku satellite as it explodes.
- Shima dies from his injuries after telling Yuki that he's always loved her. The Yamato goes to Aquarius to pick up tritium so that when Aquarius' water column nears Earth, the Yamato can combine the volatile tritium and Wave Motion Energy to cause a massive explosion and divert the water spout. As the Yamato leaves Aquarius, loaded with the tritium, the Denguil Emperor's forces appear and prepare to attack. Fortunately Desslar and his forces suddenly appear as well and destroys the Denguil Emperor’s forces. As Aquarius nears Earth and begins sending out a massive spout of water, Captain Okita, alone on the Yamato, fires the Wave Motion Gun (wired to self-destruct) and the massive explosion diverts the Aquarius wave, saving Earth, but destroying the Yamato itself.