Far in the future... or perhaps the past... humanity has spread to the stars. Due to an inability to terraform worlds and a lack of any truly viable alternatives, the species eventually turns back to Earth to re-settle. But there is no way the planet can support five hundred billion souls, and the Homecoming War is fought over who deserves the right to return. The Gaia Coalition eventually rises out of the ashes, as a government that unites the people around the idea that Earth should remain a pristine sanctuary, with no humans sullying her.
A hundred years later, humanity is dying, as the worlds they live on were never designed to support human life. Plants can never gain purchase in the ground for long, and food is running out. The only one who seems to be doing anything is Captain Harlock, the immortal pirate aboard his ghost ship Arcadia. Yama (Logan in the official English adaptations), a young man secretly in the employ of the Gaia Coalition, manages to earn a spot on the ship, where he learns that both the ship and the captain are immortal due to the dark matter engine, a gift from the alien girl who still operates it.
Furthermore, Harlock has a plan to fix everything. By detonating one hundred bombs on one hundred precise points throughout the galaxy, he can reset the Genesis Clock, turning back time and starting over. Of course, the people in power aren't particularly interested in that plan...
This film provides examples of:
- Applied Phlebotinum: Dark Matter can do basically anything, but is almost impossible to control.
- Awful Truth: Earth isn't the pristine sanctuary the Gaia Coalition claims it to be. That's a hologram projected over the planet. Earth is a scared and ravaged nightmare, torn apart by dark matter.
- Bolivian Army Ending: The movie cuts out with the crippled Arcadia preparing it's run to try and punch through the Coalation fleet and escape. After the mauling it had taken earlier, it's barely repaired enough to be spaceworthy, but the crew don't really seem concerned.
- Book-Ends: The narrator from the beginning of the movie makes another one in the end.
- Darker and Edgier: Traditionally, Harlock has gotten darker with every incarnation, and this is no exception.
- Chronic Backstabbing Disorder: Yama (Logan) betrays the Gaia Fleet after hearing Harlock's plan for a "new beginning", then betrays the Arcadia crew once he finds out Harlock had destroyed Earth and planned to end everything, only to then betray the Gaia Fleet once again after finding flowers in the middle of the dark matter-ravaged Earth
- Dub Name Change: The U.S. market release changes several character names, most significantly Yama (Logan in the adaptation). Yattaran also gets renamed Yullian.
- Eyepatch of Power: Harlock lost his eye and his best friend before becoming a space pirate. Yama/Logan takes it up along with the sword at the end.
- Fanservice: Kei's zero-gee shower scene.
- Flying Dutchman: Harlock is an immortal captain who can't leave his ghostly ship without losing his power, having to keep sailing space.
- Ghost Ship: The Arcadia can apparently disappear faster than any sort of FTL travel should allow; can summon a dark cloud around it, including in space, and can regenerate itself down to its tattered Jolly Roger flag.
- Gone Horribly Wrong: Harlock tried to create a barrier around Earth with dark matter so that no human could set foot on it again. But dark matter is unpredictable by nature, and instead ravaged the planet entirely, robbing its ability to sustain life.
- Immortality: It's not quite clear how strong Harlock is, but he doesn't age, takes at least a few bullets to the chest without stopping, and survives a drop from low atmosphere without difficulty.
- Passing the Torch/Take Up My Sword: It's implied at the end that Yama/Logan will take up the name and role of Harlock, though whether or not Harlock is dying or simply mortal now is ambiguous.
- Powered Armor: The pirates use "hardsuits" for boarding enemy vessels. Except for Kei, who just uses a fanservicey space suit. She yells at Yama/Logan when he does the same.
- Handicapped Badass: Harlock's fighting skills aren't diminished by having only one eye. Ezra is an admiral of the Gaia Corporation fleet and kicks Yama/Logan's ass in zero G. And finally, Nami acts as The Mole and gives the pirates the tactical advantage, all from her life support pod.
- Pirate Parrot: Er, Pirate Gray Thing that flies into a wall and help Harlock look dramatic.
- Politically Incorrect Villain: Not present in the English dub, but random background chatter in the original states that Ezra had his promising political career destroyed by institutionalized prejudice against the disabled. His futuristic wheelchair seems specially designed to both provide maximum mobility and to be humiliating.
- Purpose-Driven Immortality: Not Harlock, but Miime is bound to the Arcadia, and lives as long as its captain does. It doesn't actually matter who that captain is.
- Ramming Always Works: Since the Arcadia is virtually indestructible, the crew sometimes finds that the best way past an enemy ship is to simply plow right into them.
- Reset Button: Harlock's goal is to set a series of explosion throughout the universe to trigger a space-time distortion that could rewind time, giving humanity a second chance to do things right for Earth. In reality, the detonations would destroy the universe, making way for a potential new universe to take its place.
- Shoo Out the Clowns: To highlight this adaptations dark tone, Tochiro isn't even in here. He was killed in the flashback sequence.
- Space Elves: Miime is a pretty textbook case, being an ancient pointy-eared creature with bizarre powers.
- Woobie, Destroyer of Worlds: Harlock. After his plan to shield the Earth That Was permanently backfires horribly, it turns out that what he means by "resetting time" with the Genesis Clock is literally destroying the universe so a new one can be born.