Uchū Senkan Yamato: Ankoku Seidan Teikoku no Gyakushū is the second part of the "Dark Nebula series", after Uchū Senkan Yamato: Iscandar e no Tsuioku. It follows the events of the first part of the fourth Yamato movie, Be Forever Yamato. After the battle of Iscandar, the Dark Nebula Empire strikes back and invades Earth. They aim to force the earthlings into submission with the threat of a planetary neutron bomb. The bomb's trigger is located on the Empire's home planet, and so the Yamato takes off once again to find a way to prevent the bomb from exploding. Meanwhile, Yuki Mori finds herself stranded on Earth, and joins the Resistance against the invader. The game's story is based on co-creator Leiji Matsumoto's original ideas, and is quite different from the movie, with some characters meeting very different fates.

Uchū Senkan Yamato: Ankoku Seidan Teikoku no Gyakushū features real-time space battles that are very similar to its predecessor, but also new third-person phases, where the player takes direct control of a character and must navigate 3D levels to accomplish specific objectives. Like previous games of the series, the game features character-design by Keisuke Masunaga, based on the original characters created by Leiji Matsumoto. The story is told both with animated 2D movies and fully-voiced in-games cutscenes. The characters are rendered in cel-shading.