The film opens as the Earth Flagship "Blue Noah" leads the first Emigration Fleet to Amare. Suddenly, thousands of unidentified ships appear and open fire. The Earth fleet's (EDF) warships counterattack, but are quickly overwhelmed. Blue Noah is damaged critically. On one of the failing support ships, Captain Yuki Mori Kodai, wife of the protagonist Susumu Kodai, orders her ship to do an emergency warp, but for some reason, she vanishes mysteriously after the warp.
Thirty-eight-year-old Susumu Kodai, having quit the EDF sometime after Final Yamato, becomes captain of the cargo vessel "Yuki". He picks up the distress signal from the crippled Blue Noah and quickly arrives at the wreck with a boarding party. Without warning, three ships of the enemy fleet arrive. With Kodai at the helm, Blue Noah has just enough power to cover a small distance and fire one shot. Kodai's precise timing and maneuvering destroys all three ships.
Later, at the Headquarters of the EDF, Commander Sanada discusses with Kodai about the approaching black hole. Kodai also learns that his wife became lost in the battle. Sanada wants Kodai to lead the Third Emigration Fleet, saying he should follow his wife's example of volunteering.
Kodai returns home, and is met by his bitter daughter, Miyuki, who blames him for the supposed death of his wife. The two barely speak, and before Kodai can attempt to talk with her, he is called back to HQ with news about the second fleet being destroyed by three different fleets, not including the enemy fleet earlier. This means Earth now has four enemies. Kodai accepts command of the Third Emigration Fleet without hesitation, and Sanada reveals his ship: the "Yamato" itself, newly rebuilt in the Aquarius ice asteroid. After arriving at its drydock and taking his seat in the captain's chair, he makes a solemn vow to find his wife, refusing to believe she is dead. On the other side of the galaxy, the leader of the enemy fleets and the fleet that attacked the Blue Noah is revealed to be the SUS. Metzler, the leader of the SUS, deceived the others that Earth is an invader, and they are barbarians. However, one leader—Gouri, admiral of a fleet belonging to the planet Ethos—is unsure.
The Yamato takes off and joins the fleet, taking its place at the front as Flagship. In the planning room, the crew lays out the mission. The plan is to slingshot around a small black hole, BH199, and boost the arks and warships into high warp, propelling them to Amare much faster than usual. There is no other option, as there are enemy ships lurking around them and the previous fleets were destroyed at this area. Gouri watches the first group of arks slingshot and warp, and then, still unsure, orders an attack. Soon, all the fleets open fire in a frantic battle, damaging warships in each side.
However, when Gouri witnesses the Yamato putting herself in harm's way to defend an ark, Gouri concludes that he has been lied to. He orders his fleets to cease firing and retreat, since the action of the Yamato is "not how barbarians act". He contacts Kodai and tells him that they were misled, twisted to do the bidding of the SUS. Seeing that the EDF fleet fought honorably, Gouri allows them to go in peace. It had some repercussions—he is later threatened by Barlsman, a SUS leader. However, Gouri holds his ground.
The third EDF fleet successfully arrives at Amare, much to the joy of HQ and the citizens of Earth. However, not all is well. SUS launches an attack on Amare, dropping bombs on its cities. Gouri, in an attempt to reclaim his honor and save Amare, rams his vessel into the SUS flagship, destroying it and killing him in the process. Yamato is ordered by General Pascal not to interfere, as it would make Amare-SUS relations worse. Kodai, remembering that his wife always fought injustice, is inspired and informs the Queen Iriya of Amare of his intention to declare war on the SUS. The Yamato launches and blows the SUS bombers away easily. The Queen is brought to tears and thanks Kodai and his crew for their bravery. General Pascal is also inspired, and joins the EDF fleet for one final battle: an assault on the nearby SUS space fortress. If it is destroyed, then the SUS will lose control over everything.
Earth and Amare fleets warp in, and are plunged into battle. Once again, the EDF fleet takes heavy damage, and the Amare fleet is completely wiped out. During the long battle, the Yamato's First Officer sacrifices himself and disables the defensive energy shield around the fortress by ramming it with the Shinano, Yamato's auxiliary ship. The Yamato prepares its Wave Motion Gun for the first time, and with five powerful shots, destroys the fortress. Then, an immense ship emerges from the bowels of the destroyed fortress, unleashing one superweapon after another. It is only stopped when Kodai, realizing that the power source is the artificial sun behind it, uses the final available shot of the Wave Motion Gun on it, collapsing the sun and turning it into a black hole. The Yamato escapes, while the enemy ship—with all of the SUS leaders in it—is torn apart and sucked into it. Metzler escaped the destruction of the SUS space fortress, and appears to the Yamato crew and reveals himself and the people of the SUS as energy beings that can change form, being sent to this galaxy from another universe. He then disappears.
The Yamato warps back to Earth, and the energy being Metzler appears again. He reveals that the black hole headed for Earth is artificially created and controlled: it will serve as a portal to "steal" Earth and take its resources, since they cannot be found in his world. Kodai realizes that it must have a power source. 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. Earth can now be repopulated and the arks can return home. Kodai also reconciles with his daughter in the end.
In March 2002, a Tokyo court ruled that Yoshinobu Nishizaki legally owned the Yamato copyrights. Nishizaki and Matsumoto eventually settled; Nishizaki began work on a new movie, while Matsumoto planned a new Yamato series, both to take place after their respective stories. However, additional legal conflicts stalled both projects until August 2008, when Nishizaki announced plans for the release of his film on December 12, 2009.
The production makes ample use of CGI for the space battle scenes. Out of the 1860 cuts (shots) in the new film, 700 are being produced with computer graphics. 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 size will be mostly unchanged at 263 metres in length and 62,000 tons in mass. 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.
This film sees the reappearance of the Yamato's counter-attack missiles, not otherwise seen since the mission to Iscandar (first TV season). The defensive shield which they form upon detonation is now energy-based.
Among the new technological items is a gravity-assisted warp process called a "long warp". 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.
As far as other ships go, a new model Earth battleship, "Super Andromeda", appears, as well as the Earth flagship, Blue Noah.Susumu Kodai (CV: Kōichi Yamadera), Captain of the Yamato, former Battle Commander.
Yuki Mori Kodai (CV: Noriko Yume), Susumu's wife and former Radar/Computer Operator of the Yamato, captain of an escort battleship with the First Emigration Fleet, presumed lost in action.
Tasuke Tokugawa (CV: Tōru Furuya), former Engineer of the Yamato, leaves his position as a commanding officer at the Earth Defense Force's Moonbase to become Chief Engineer of the Yamato.
Shiro Sanada (CV: Takeshi Aono), Secretary of Science for the Earth Federation, former Science Officer of the Yamato.
Jiro Shima (CV: Ryōtarō Okiayu), younger brother of Daisuke Shima, head of the Earth Federation's Migration Fleet.
Dr. Sakezou Sado (CV: Ichirō Nagai) and Analyzer (CV: Kenichi Ogata), remain on Earth to watch over Dr. Sado's Safari Park.
Captain Jūzō Okita (CV: Gorō Naya, stock footage)
Miyuki Kodai (CV: Ayumi Fujimura) daughter of Kodai and Yuki, assistant to Dr. Sado.
Kosaku Omura (CV: Chafurin), Vice Captain of the Yamato.
Minoru Goda (CV: Akimitsu Takase), Artillery Specialist of the Yamato, replacing Nanbu.
Atsushi Kobayashi (CV: Daisuke Namikawa), Chief Pilot of the Yamato's Cosmo Pulser Squad, replacing Katou.
Miharu Sasaki (CV: Fuyuka Ōura), Ship Doctor and Cosmo Pulser Pilot.
Ryohei Nakanishi (CV: Kappei Yamaguchi), Communication Specialist of the Yamato, replaces Aihara.
Yoichi Sakurai (CV: Kenji Nojima), Radar Specialist of the Yamato, replaces Ohta.
Ryo Kamijo (CV: Kentarō Itō), New Tactical Commander of the Yamato.
Saburo Kinoshita (CV: Kōsuke Toriumi), New Science Officer of the Yamato.
Maho Orihara (CV: Ryōka Yuzuki), Chief Navigator of the Yamato, replaces the late Daisuke Shima.
Sho and So Tenma (CV: Daisuke Sakaguchi), twin brothers, Engineers under Tasuke on the Yamato.
Blue Noah Captain (CV: Osamu Kobayashi), captain of the Space Carrier Blue Noah
Queen Iriya (CV: Atsuko Tanaka) and General Pascal (CV: Kazuhiko Inoue) of Planet Amahr.
Admiral Metzlar (CV: Hiroshi Yanaka) and Commander-in-Chief Balzman (CV: Shōzō Iizuka) of the SUS Empire.
Admiral Gorui (CV: Masatō Ibu) and Captain Shihgal (CV: Takehito Koyasu) of Planet Ethos.
The film debuted #7 at the Japanese box office but moved slowly off the charts a week later.
A reviewer on SciFiJapan said that he was pleased with the film, and that it gave the series a reboot that it had missed for 30 years. He went on to say, while the romance was definitely toned down, the action made up for it. "Computer enhancement works its greatest magic in scenes of outer space, especially those of black holes. The beauty and imagination of these scenes are nothing less than spectacular." However, he was disappointed by the enemy ship designs. "The weakest visual element in the film is the design of the enemy fleets. Yamato history is populated with dozens of sleek and exciting spaceship designs, so these new ship designs are a rather jarring and unimaginative change of pace." The reviewer concluded with, "SPACE BATTLESHIP YAMATO: RESURRECTION brings the famed space battleship back to the big screen in all its former glory, setting the stage for a live action version which will hit screen in Japan later this year. 2010 promises to be a banner year for Yamato fans, new and old."
On StarBlazers.com, a positive reviewer said that "I snapped to full attention for the finale. I can't say why, but it suddenly felt more like a true Yamato story than it did before. It gave me an immediate jolt of energy and took me all the way home, which makes it my favorite part." The review finished with this, referring to the character development: "To Nishizaki's credit, he tipped this in his Animage interview, saying his intention was to simply establish the new crew so they can be further developed "next time." I'd love to see a TV series spin off from this, but I have no idea if such a thing is possible. One thing's for sure: I'll be happy to see Part 2 in any Japanese theater."
The film was released on Region 2 DVD, UMD, and Blu-ray on July 23, 2010. 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.