The day of their return is the anniversary of Captain Okita's death. Kodai, attending the memorial at the Heroes' Hill, expresses his concerns about the new threat and his doubts about Earth's complacent prosperity.
During Earth's major power outage, Kodai witnesses a mysterious reconnaissance aircraft and learns that the analyzed powerful transmission is warning of a space crisis.
The headquarters staff, detecting the gathering of former crew members at the Yamato, issues a disbandment order, but Kodai refuses it. The staff member insists on forceful measures even when the commander requests a peaceful resolution.
The Yamato is bustling with activity after accommodating Kato's Cosmo Tiger squadron. Yuki Mori is also aboard. Kodai issues an order for her to disembark, but then assigns her to her former duties as she changes into her space suit.
The 11th planet base at the outermost edge of the solar system is under attack by the Nazca reconnaissance fleet of the comet empire. The Yamato, rushing to their aid, destroys the enemy battle fleet with its main gun.
Inside the Yamato, conflict arises between the space cavalry unit, who disregards discipline, and the Yamato crew. At that time, the time-delay radar detects an enemy ship from two hours ago, and the Yamato goes on alert.
After leaving the solar system, the Yamato receives a transmission from Teresa and attempts a short warp. However, the transmission is a trap set by Admiral Goland of the comet empire's Telezart forward fleet.
Discovering an enemy combat boat, Kodai orders Kato and Yamamoto to launch to obtain enemy intelligence. However, Yamamoto's aircraft is stolen by Saito, who harbors a grudge against the enemy.
After disengaging the asteroid ring and barely passing through the asteroid belt, the Yamato finds a large enemy fleet waiting in ambush. Despite the energy shortage, Sanada has Kodai order the firing of the wave motion gun.
The Yamato, undergoing repairs while navigating, encounters space fireflies. The space fireflies brought aboard by a rookie and Analyzer for viewing turn out to be bacteria that corrode metal.
The battle carrier that has cornered the Yamato is also infested with "space fireflies" and retreats. To remove the space fireflies, the Yamato enters the interior of a hollow asteroid. However, it is a trap set by Dessler.
The Dessler fleet suddenly withdraws, and the Yamato finally arrives at Planet Telezart. While countering missile attacks from the remaining base, Kodai has the space cavalry unit land in the hollow city below the surface.
The space cavalry unit is in desperate situation under the gunfire of the appearing Zabaibal tank corps, but they begin assembling the multiple cannons transported by Kodai and his team, and start counterattacking by capturing tanks.
After annihilating Zabaibal's tank corps, Kodai and his team meet with Teresa in the palace Telezarium. After waiting for Shima to arrive, she tells them about the white comet Gatlantis Empire.
As launch preparations are underway on the Yamato, Teresa's high-power transmission comes through. Kodai sends Shima to Teresa to confirm its meaning. Concerned about her, Shima invites her to the Yamato.
The Yamato, rushing to return, executes a 2000 light-year warp. However, the emperor orders the advance of the fleet of Valsey, which has gone ahead, and a triple-speed advance for the comet empire.
Two days before convergence, the Yamato returns to the solar system, where Saito, hoping to stop by the 11th planet, starts a fight with the crew. Kodai issues a compassionate order for exploration.
The Yamato, leading the Earth carrier fleet, receives orders from Commander-in-Chief Hijikata to launch a surprise attack on the enemy aircraft carrier fleet behind the enemy fleet.
The Yamato, having escaped the explosion, lands at the Jupiter moon Ganymede base and begins major repair work. Earth, having lost its fleet, falls into chaos with evacuating citizens.
The city fortress, the Yamato's warp target, is already approaching Earth. There, Gamilas attack aircraft appear. Dessler lays magnetic mines using an instantaneous matter transfer device, sealing off the wave motion gun.
Kodai, confronting Dessler, passes out from the pain of his arm injured during the intrusion. Yuki Mori, who rushes to him involuntarily, points a gun at Dessler and puts on a brave front while worrying about Kodai.
The super-giant battleship, 12 kilometers long, that emerges from the city fortress silences the Yamato with its gunfire and begins attacking various parts of Earth with its lower super-giant cannon.
Only 18 survivors remain on the Yamato, which has lost its attack capabilities. Kodai, who orders everyone to abandon ship, launches two lifeboats and then jumps onto the deck alone.
