The planet to which Earth's population is being moved is called Amare, ruled by Queen Iriya, some 27,000 light years away in the Sairam star system.

Kodai accepts command of the Third Emigration Fleet, and Sanada reveals his ship: the Yamato itself, newly rebuilt in the Aquarius ice asteroid.

The plan is to slingshot around a small black hole, BH199, and boost the arks and warships into high warp, propelling them to Amarh much faster than usual.

The Furide Fleet begins a massive bombardment on the Yamato and the battleship responded with all guns blazing but 3 Furide Ships, the Furide Flagship among the 3, strayed off from the battle and straight for the Vulnerable Unarmed Arks and begins a bombardment of missiles, the Yamato notices the stray ships but is under heavy fire preventing the Battleship from moving, with quick thinking the Battleship deploys 3 docked heavy bombers and managed to successfully destroy 2 of the unsuspecting Furide Ships, one of the heavy bombers continued firing on the last surviving Furide ship which was the Flagship of the Furides and succeed in destroying the alien vessel killing the Furide Commander before they can cause more harm to the fleeing arks, meanwhile the Second Group of Escort Ships confronts the Ethos Fleet and started fighting taking losses on both sides, the Yamato was continuously hit hard by the Furide, thinking quick, Kodai orders a Missile Barrage which destroyed a large portion of the Furide Fleet, on board the Ethos Flagship Gouri notices the ferociousity of the Yamato in battle which inspires the Escort Fleet in battle, Gouri then orders the Fleets to concentrate on the Yamato, meanwhile the SUS Fleet which didn't participate the Battle, on board the SUS Flagship with Meltzlar onboard was quite surprised to see many Alliance Ships being destroyed, soon enough Escort Ships came to assist the Yamato in fighting the leaderless Furide Fleet, with majority of the arks successfully slingshoted from the black hole, Kodai orders the Escort Fleets to regroup and head for the black hole with the Yamato covering their escape, many ships were damaged while escaping, the Furide and Beldel Fleets turns their attention on the Yamato punishing the Battleship with barrage of fire, Ryo Kamijo, the Gunnery Officer of the Battleship prepares the Wave Motion Gun in anger only to be stopped with a slap from Kodai, explaining to him that if they fire the Gun, the Yamato will be drained of Energy leaving the Battleship Defenseless, obeying the Captain, the Gunnery officer turns off the Wave Motion Gun.

As the sun sets in the evening, the Bridge crew of the Yamato wondered if the people of Amare will call their Moon, Earth.

The Amare came to hate the SUS but couldn't do anytjing as they were supplying the SUS with resources revealing that the Planet of Amare contain a rare Material which is sought by the SUS, in return the people of Amare receive protection from the SUS, after talking to the Queen Kodai was confronted by an Armed Amarean who is revealed to be General Pascal the leader of the Amare Military, he forces Kodai into a room, Kodai obeys the order only to be faced with 3 Armed Royal Guards upon entering, General Pascal demands that the Humans leave or they will be punished by the Alliance or destroy Amare, kodai refuses, the Royal Guards threats to kill him but the building shakes, realizing the SUS is attacking the City, General Pascal demands Kodai not to interfere, as it would make Amare-SUS relations worse.

The SUS launches an Airstrike on the Amare City, dropping bombs on the streets killing numerous civilians, two Massive SUS Tanks and one Colossal SUS Siege Tank plowed the streets destroying buildings, the Amare Police along with armed citizens fought back, the Yamato floating at the distance, The Bridge crew was shocked, Ryo kamijo the gunnery officer demands the First officer to launch the Yamato to battle but they notices the SUS Bombers retreating, Kodai arrived on the bridge after returning from the City, he explains to the Crew of what he learned which stunned everyone, the Yamato goes on standby, the Yamato detects a second of wave of Bombers, this time with fighters among the groups of bombers they began their bombardment on the helpless city killing more civilians, the Amare Army now joining the fight against the SUS.

Back on the Yamato Kodak received a message from Gouri, both former enemies greeted each other with Salute, Gouri explains to Kodak of he's intentions on turning against the SUS and the Alliance, being pressed by the Alliance in exchange for "peace" which is how the Alliance operates, ending with a Salute, on board the SUS Flagship, Metzlar gives a big thumbs down and the SUS Fleet begins descending on the Ethos Fleet, both sides open fire on each other in a fury blaze of beams, Gouri aims for the Flagship of the SUS Maya on a Suicide Run, the Ethos Flagship bursts in speed towards the Maya in a final charge of honor, Kodai was shocked at what Gouri is doing, a vengeful Metzlar orders the Fleet to target the Ethos Flagship but the Resilient Ethos ship absorbs large amounts of fire and even ram pass a SUS Ship scaring Metzlar, the Ethos Flagship rams the Maya destroying the massive SUS Flagship killing Gouri and he's First Officer along with everyone else on both ships, but Metzlar managed to escaped with some surviving crew, both sides disengaged... On board the Yamato Kodai salutes the fallen Admiral in silence, at the Amare City, Queen Iriya asked Pascal for he's thoughts on Ethos attacking the SUS which he didn't answer, a fellow Royal Guard reported that mass amounts of Citizens are gathered outside the Palace and their numbers are increasing, outside the streets the SUS Tanks slowly approaches the Palace firing at buildings, a fellow human survivor was caught in the crossfire, outside the Palace, the crowds cheer and wants to join the Yamato in battle.

Back on the Yamato Kodai remembering that his wife always fought injustice, is inspired and informs Queen Iriya of his intention to declare war on the SUS.

Outside the Fortress, a massive combined Furide and Beldel and SUS Fleet stands ready and waits for their opponents to arrive for battle.

The combined Fleet led by the Yamato and the Amare Flagship warps in, the Yamato deploys its Squadrons of fighters and heavy bombers, both sides starts firing on each other losing ships, the Squadrons of the Yamato faces off with Squadrons from the Beldel Fleet in a massive Dogfight, the Yamato then suffers damage from enemy Fire losing one of its main gun turrets, the ship's Warp Core starts to malfunction but was quickly fixed by the Chief Engineer Saving the Battleship from destruction, as the Battle rages into dangerous close quarters, kodai orders the Yamato To break off and aim for the center with cover for their squadrons, behind the combined enemy fleet, the SUS space fortress reveals itself from the mist of red clouds, surrounded by 5 massive pillars, Kodai surprised by the size of the fortress, orders Maho the Chief Navigator to analyse the fortress, inside the fortress, Barlsman was disappointed with Metzlar's tactics which he replied by ordering the Fortress Crew to prepare the Neutron Beam Cannons to fire on the Combined Earth and Amare fleet, the crew refuses as Allied ships were on the line of fire but Metzlar forces them to fire, outside the fortress, the 5 pillars are revealed to be the neutron guns, 2 of the pillars deployed its massive Gun barrel and fires a massive surge of neutron energy at the Fleets destroying almost all of the alliance ships, General Pascal orders the Amare Fleet to defend the Yamato the beam destroys the entire Amare Fleet and a large portion of the Escort Fleet, the Flagship of the Amare fleet was severely damaged defending the Battleship from the neutron beam with its shield, on board the burning Amare flagship, a dying Pascal bids the Yamato Good luck, the ship explodes, the bridge crew of the battleship was in total shock that the SUS fired on their own and was not so surprised when the surviving ships of the alliance turns and retreats from the battlefield, inside the fortress Metzlar requests they fire all 5 of the Neutron Guns on the Escort Fleet which Barlsman approves, the other 4 Pillars deploys their gun barrels and fires in unison, the Yamato and her Squadrons managed to escape the beam as they tear through the battlefield destroying the remaining Escort Ships, the Yamato fires a massive barrage on the fortress but they were deflected by its impenetrable shield, kodai orders the squadrons back to the ship, Maho reports to bridge about her findings and reveals to the crew about the inner workings of the space fortress, realising that the 5 pillars are also the shield generators for the fortress, the Yamato's First Officer requests to borrow the Shinano, Yamato's auxiliary ship but kodai refuses but the First Officer deliberately volunteers himself for this which kodai agrees, the Shinano fires a barrage of Wave Motion Missiles but they were ineffective, the Shinano was greeted with a massive barrage of anti air fire from 2 pillars damaging the Shinano, the First Officer already wounded, sacrifices himself and disables the defensive energy shield around the fortress by ramming destroying the Shinano shattering the shield like glass, inside the fortress a fearful Barlsman and Metzlar watch in horror while Kodai gives a Salute, he then orders the Crew to start up the wave motion gun while the fortress aims its Pillars on the Yamato, with the Wave Motion Gun ready, the Yamato unleashes five powerful shots, destroying the pillars revealing a massive sea and the main SUS Fortress sinks.

The Wave Motion Gun automatically reconfigured to enable it to fire all six shots in one go, a risky decision that could destroy the ship, but the crew unanimously agree that saving Earth is more important.

The Yamato dives into the black hole, and as it reaches the core, the Wave Motion Gun fires, destroying the artificial weapon in a gigantic implosion.

The blast from the Wave Motion Gun had ruptured and damaged the Yamato bow and front section; the third bridge (where the ship's navigation room resides) also suffers serious damage and is exposed to space, killing Chief Navigator Maho Orihara, who was working in it, and her assistants; but the ship is still space-worthy and orbits Earth in triumph.

However, additional legal conflicts stalled both projects until August 2008, when Nishizaki announced plans for the release of his film on December 12, 2009.

In particular, the battle scenes use composite 3D sequences and computer graphics; Nishizaki had established a new studio called Enagio in 2008 just to produce this film.

The Yamato's signature wave-motion gun, which can take out an entire fleet, but which then leaves the ship drained of power — and vulnerable, has been improved to optionally fire six smaller shots in succession.

Other defensive features include the battleship's armor, which is far stronger than originally depicted during the Battle of the Rainbow Nebula—in the film, the Yamato withstood a massive concentrated barrage from both Furide and Beldel Fleets and survived, and suffered minor to moderate damage during the battle against the SUS Dimensional Fortress.

The visual special effects for the Yamato undergoing warp have been improved, and now resemble something akin to Farscape's starburst.

The Yamato's new multistage Wave Motion Gun can now fire a spectacular spray of tachyon-based energy in a succession of six bursts.

Yamato's infamous third bridge is now painted blue, and houses more expensive gadgets to get blown up such as a 3-dimensional navigational cartography room.

[11] The anime will not be licensed by Funimation Entertainment due to a miscommunication and the announcement was actually referring to the 2010 live-action film Space Battleship Yamato.