Trapped under rubble and deprived of sensors, the crew focuses on repairing the damage when an alarming report arrives from the outside. The Gatlantis are amassing thousands of ships in orbit around the artificial sun, and Analyzer's conclusion forces Kodai to contemplate a dramatic outcome.

Yamato works under fire to break up the rocky crust imprisoning the planet Terezart, while Cosmo Marines and fighter pilots fight against Gatlantis' massively armed ground forces. Kodai, Sanada, and Saito venture under the surface of Terezart to meet the goddess Teresa.

Just as Gatlantis prepares to slaughter the Terran fleet, Wave Motion Gun shots crash through Saturn's rings and destroy a portion of the Gatlantis fleet. Terran ships jump through the rocks and begin their assault, as more de-warp into the system. Before the fleets can fight for too long, the White Comet jumps into Saturn and destroys a chunk of it. The Wave Motion fleet scattered, the Yamato attempts to use the Wave Motion Gun to disable the White Comet, but are instead knocked out of commission and dragged into the white abyss.

Katsuragi tells the AI to reveal everything about the planet, and Gatlantis. It is revealed to Kodai and the crew that Gatlantis are artificial, and that they have a major kill switch right under their leaders feet. Zwordar orders the planet Yamato is on to be destroyed. At the Mars Defence Line, Admiral Yamanami with an upgraded Andromeda, fights through hordes of enemy ships in an attempt to reach the centre of the White Comet. He sees that Yamato is alive, and using his ship as a sacrifice, rescues Yamato.

Zwordar activates Golem, which wipes out the Gatlantis race, all but himself. He is absorbed into the Ark of Destruction, which begins to transform. The Yamato manages to escape the area, but the gravity anchor is holding them. Keyman, using a Wave Motion torpedo, sacrifices himself to free Yamato. Too damaged to continue, the Yamato is evacuated. Using the now bleeding core of the Yamato, Kodai, as well as Yuki, use the Yamato to destroy what remains of the Ark of Destruction, ending the war.