A planet called Telezart comes under attack by a race known as the Gatlantis, who wish to conquer the world and use its power for their own gain. Meanwhile, Earth and Garmillas, now allies after their ten year war, fight side by side to retake a world lost. The Yamato crew are angered by the revelation of the Andromeda class battleship. The crew receive a vision from a planet called Telezart, calling for their aid.
Tensions run high amongst the Terran and Garmillan factions. Four new Andromeda class battleships are revealed and launched, a blunt show of force. The Yamato crew reunite at heroes hill, to honour Captain Juzo Okita, the crew that have passed, and the day of their return. They discuss a vision they all saw, and their next move. Susumu Kodai is asked to go to the Moon by Garmillan liaison, Keyman.
After making it to the Moon, Governor Barrell of the Garmillas faction informs Kodai that there is something he needs to witness. He orders Keyman to escort him to the Time Fault, which is a sub-dimension where time is 10x faster than in the outside world. There, the Wave-Motion Gun Fleet is being constructed, much to Kodai's chagrin.
The Yamato crew is resolute in their resolve, and they have decided to follow their hearts and head to the world of Telezart, where the cosmo wave came from. This leads to the Yamato crew leading a mutiny against the United Nations Cosmo Force, and stealing the Yamato to head to Telezart. They use the underground docks of the Garmillan wartime city to launch the Yamato.
The Yamato heads for deep space, but cannot warp until their engine is repaired. The former fighter squadron pilots on a training exercise with the Andromeda fleet go AWOL, and head to Yamato. The Andromeda then arrives to attempt to disable the Yamato, but her crews resolve is strong and she blows past it. UNCF command rescinds their order to stop Yamato, and then tells them to head to Telezart as a mission.
Yamato finds a lifeboat, one launched from the 11th planet of the Solar System, Brumis. Shiori Nagakura, a space marine, recounts how Gatlantis launched a surprise attack against the colony world. Many civilians are killed in the opening moments of the battle. The survivors battle Gatlantis forces, and are slowly overwhelmed. Before they are executed, the Yamato warps in a successfully evacuates the civilians and remaining marines.
A large fleet of Gatlantis warships have warped out over Brumis. They begin taking a large cone shape above the planet. The Yamato, trapped underground, devises a plan of escape. Analyzer, the Yamato's Autonomous Unit, along with Shiro Sanada discern that the cone shaped fleet is a large gun, aimed at Earth. With no other choice, the Yamato launches, and against the promise of Juzo Okita, fires the wave motion gun, disabling the fleet.
The Yamato leaves Brumis and heads to the planet Stravaze, where it plans to link with a Garmillan fleet that will take the civilians back to Earth. During the exchange of ships, they come under attack by rebel Garmillan forces, seeking to destroy the former ruler, Desslers, shadow from Garmillas.
In a Akerius ruin on Stravaze, Gatlantis Emperor Zwordar explains how he will force Kodai to choose the mass lives of the civilians, or Mori Yuki, his love. The artificial body detonates, but Hajime Saito, one of the Cosmo Marines, saves Kodai from the explosion. Kodai is torn between which ship to save, and which to sacrifice. Yuki offers herself as sacrifice. The Yamato uses the Wave Motion Gun and collapses the rift, saving all lives.
After escaping the near tragedy of Stravaze, the Yamato resumes course to Telezart. En-route, what seemingly appear to be fireflies begin to float around and into the Yamato. The crew, in a trance-like state, capture these fireflies and keep them in containers around the ship. This sends the crew into a hyper-emotional state, which makes them act more irrationally. With the help of Keyman, they are able to neutralize the infestation.
The Gatlantis fleet at Brumis gives chase to the Yamato, bent on revenge. They are swiftly destroyed by Abelt Dessler, who wishes to ‘prove’ himself to the Gatlantis Emperor. He then hunts down the Yamato, using long-range missiles to send them on a particular planned path. The Yamato warps into a sub-dimension, one born of a dying star. Dessler uses his Wave Motion gun to try and destroy Yamato; however, they ride the energy like a wave and use it to escape.
The Yamato is ambushed by the White Comet, Gatlantis's homeworld. The ship is pulled into the Comet, seemingly by unnatural forces. The silver priestess of Gatlantis, Sabera, resonates with a sleeper-agent of a similar design, which causes her mind to crash. Zworder murders Sabera, and allows Yamato to escape.
Arriving at Telezart, the Kodai and the crew devise a plan to punch through the Gatlantis fleet blockading the world. Using a warp booster plane and mechanized units, they jump behind enemy lines and destroy the rear-guard. The main Gatlantis force uses a specialized missile to destabilize Yamato. With the mechanized units holding the Yamato, Kodai shows his resolve and fires the Wave Motion Gun, destroying the Gatlantis fleet.
The Gatlantis have a ground assault force, which begins to attack Yamato, who pulls back to a safe range. Some mechanized units head to ground to establish a landing zone. The onslaught is heavy, until Saito drops a few large asteroids on the enemy tank brigade, forcing them into close combat. With the enemy forces destroyed, Telezart fully reveals itself.
Teresa reads through Desslers mind, dredging up old memories from a time long passed. Kodai sneaks up behind him, intent on ending him for good. Keyman arrives minutes later, wanting to find out the truth. It is revealed that he himself is a Dessler, and nephew to Albelt Dessler. Keyman turns his gun on Kodai and knocks him unconscious.
Keyman finds himself questioning his choices, and goes back to Teresa to seek guidance. Albelt also finds that he himself requires answers, and also seeks Teresa's counsel, even if he does not necessarily want it. Keyman, now having a new purpose, frees the captives aboard Dessler's ship and flees back to the Yamato.
Gatlantis have begun their second phase of invading the Solar System, by sending an advanced force to Saturn. The UNCF fleet moves to defend Saturn, but are slowly overwhelmed. On Earth, the President of Terra declares open war with Gatlantis. Admiral Yamanami, in charge of Andromeda, takes his fleets and counter-attacks against Gatlantis.
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.
The Space Battleship Ginga, a Yamato class battleship, begins counter-attack operations against Gatlantis. Gatlantis attempt to thwart Ginga and her fleet, but are ultimately wiped out. Meanwhile, Yamato has crashed on a world within the White Comet, and the crew are exploring the ancient ruins on the planet.
Kodai and Keyman have departed Yamato in search for answers. They stumble across ancient ruins, in which an old AI is guarding vital information about Gatlantis. The AI takes over Analyzers body, and wishes to speak to the last human of this world. They take the AI to Toko Katsuragi, the Gatlantis spy, who is pure blood. Elsewhere, Zwordar orders the White Comet to warp to Mars Defence Line.
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.
The Yamato receives repairs and upgrades at the shipyard above Mars, where much of Ginga's parts are transferred over. Repaired, the Yamato sets out to chase after the White Comet and end the war once and for all. However, before the Yamato can get far, she is attacked by Dessler, who struck a deal with Gatlantis. Kodai orders the Yamato to warp into Desslers ships bow, where they can board and disable the ship.
Keyman and Dessler face off on the bridge. The Gatlantis envoy attempts to force Keyman to kill Dessler, so he can see their emotions. Kodai arrives on the scene and attempts to stop the conflict, and is nearly shot dead for it. Yuki, who had been tailing Kodai, leaps out from behind cover and takes his bullet. The grief overwhelming, the Gatlantis envoy plans to stand down until a guard executes him. Dessler bids Yamato a farewell, and leaves the area for good. Meanwhile, Gatlantis has jumped ahead and has begun to invade Earth.
The Yamato warps to Earth, just ahead of the White Comet. Using Dessler's ship as a shield, they fire the Transit Wave Motion Gun, which destroys the protective layers surrounding the Gatlantis homeworld. Garmillas warps in to defend the planet while the Yamato sneaks on ahead. Yamato charges through the White Comet, becoming heavily damaged. The fighter squadron make it a bit further, and head to the throne room, where they come face to face with Zwordar.
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.
Six months have passed since the Gatlantis war. The surviving Yamato crew are at Heroes Hill, mourning their lost comrades. In the Time Fault Factory, the Yamato warps out from a higher dimension. Kodai and Yuki are alive, but trapped in this higher dimension. Yamanami, Sanada, and a few others attempt to convince the Earth Council to let them use the Time Fault as a booster, to save Kodai and Yuki. It's put to a vote, and the Yamato Crew win unanimously. Yamato is boosted to the higher dimension, and Kodai and Yuki are rescued. The Yamato returns to real-space and returns to Earth.
