公元2977年。 人类已经掌握了进入太空所必需的科学技术，并且利用机器人来耕种行星和生产食物，我们正在进入一个前所未有的富足时代。哈洛克船长，他的名字在地球上以太空海盗而闻名……

第七惑星出发的运输船队遭到了不明飞碟的攻击。地球将这视为哈洛克的行动，试图用哈洛克所称的 "大切な友から預かった" 少女玛由作为诱饵来捕获他。

城市陷入了侵略者的来袭物体所带来的恐慌。在观看这一情景的同时，有台羽博士和他的儿子正陪伴的克斯科教授，直觉地认为这个来袭物体是侵略者投放的旗帜，一种主张地球占有权的 "标志"。

虽然哈洛克邀请了他，但正因为是海盗而离开了阿卡迪亚号。 与此同时，库兹科教授破译了三角旗上的文字，并告诉总理和其他政府官员，马佐内正在瞄准地球，他们认为地球是他们的第二故乡。

虽然哈洛克加入了阿卡迪亚号的船员，但当哈洛克告诉他“你现在不需要做任何事，只是玩玩而已”时，正感到很困惑。 而且，船员们都是为所欲为，这与正志心目中的阿卡迪亚号形象完全相反。

“莱佛士女王”……这句话让马佐恩士兵爆发了。哈洛克觉得需要收集更多信息，击落了一艘马佐恩战舰以确认其适用性，并让船员收集了残骸。从分析结果来看通过对这些碎片的研究，他们发现了马佐内曾干扰过古代地球的可能性。

从太空看到的地球正在表现出奇怪的反应，因此哈洛克和他的朋友们前往以魔鬼三角闻名的百慕大海域进行调查。哈洛克和他的朋友们在海底发现了一座据信是马佐内建造的金字塔. 探索内部并推断 Mazone 是一种以植物为基础的生命形式。

信号旗和金字塔发出信号，旨在引导马佐内本身。 哈洛克感受到了直接对抗，重申他的使命是保护设计阿卡迪亚的最好朋友的女儿麻友，并返回地球与她见面。

零博士从战俘的头发样本中发现，具有类似汁液的植物分布在古代遗址周围。 为了揭开古代遗迹与马佐内之间的关系，哈洛克命令正和副酋长亚塔兰去采购燃烧的陶器。

哈洛克深信马佐尼人沉睡在地球各地的丛林中，决定返回海盗岛。在那里，部下在南美被杀的阿勒奎亚斯发动了一场复仇战争。在此期间，……当正看到另一名飞行员萝拉的脸，他犹豫了一下要不要扣动导弹的扳机……

阿卡迪亚号继续顺利驶向金星。 途中，哈洛克和他的朋友们发现了一艘遇险的马佐尼船，并从船上救出了被俘的飞行员劳拉。 然而，就在前面的士兵自爆的时候，劳拉却只是露出了令人毛骨悚然的笑容……

Tadashi is upset at himself for talking about the Arcadia to Lola. Then he begins practicing like mad so he can shoot in time next battle. Examining Venus, they spot formations on a fossilized continent that look like Nazca drawings. They follow it onwards to the base and find drawings about Earth from over 180,000,000 years ago.

The Arcadia heads back to Earth to investigate a third signal being emitted from the Sargasso Sea. There, the witch Aman, who was waiting for the Arcadia, wages an attack using a 1945 Imperial Japanese naval ship. Harlock, curious as to how this phenomenon occurred, sets off to investigate at the bottom of the sea

Commander Kiruta takes Mayu with him. Desperate to find her, Harlock receives a message from Commander Kiruta. "Fly to Cairo, Egypt.", "Board a Cessna.", "The Arcadia is to wait in the Valley of the Dead.

An aurora borealis of clear artificial origin disturbs the communications and electromagnetic systems of Arcadia, at the North Pole a strange being that carries out Rafflesia's commands manages to get Arcadia stuck in the middle of the eternal ice: Kirita tries to take advantage of the situation but his bombing only helps Harlock's spaceship free itself.

The operator, Kei Yuki, goes to visit her parents' grave. There, her father's ex-pupil, Kazuya, shows up. They had attempted to make a space colony not out of machines, but with nature exactly akin to Earth's. However, the experiment failed and Kazuya, the lone survivor, returned to blame her father.

Upon finding a message in a bottle floating in space that contains an SOS message from Captain Yamanaka of the Braves ship, the Arcadia sets off for the Horsehead Nebula.

he operator, Kei Yuki, goes to visit her parents' grave. There, her father's ex-pupil, Kazuya, shows up. They had attempted to make a space colony not out of machines, but with nature exactly akin to Earth's. However, the experiment failed and Kazuya, the lone survivor, returned to blame her father who had lost his life there. But now he regrets this and wants to continue the research

There are supposed to be forty-two crewman aboard the Arcadia. Searching their true colors, they try to read the minds of all at the Horsehead Nebula. After reading them all, they decide to take the next measures.

Miime's old planet is named Jura, and it was once devastated by a nuclear attack. Making one of her occasional visits to her hometown, Miime and Harlock are once again ensnared in a Mazone trap.

Arcadia, having returned to the interior of the solar system, is now located near Jupiter (astronomy); strange beings, who however immediately reveal themselves not to be Mazonians, attack her. Tadashi manages to capture alive Captain Goram (Zoru), belonging to the army of Tobaga, a small planet located in the main asteroid belt orbiting between Jupiter and Mars (planet).

Harlock is studying the precious news left to him by Goram regarding the composition of the Mazonian fleet. Rafflesia has caused a pennant to fall onto the surface of Mars coming from the Andromeda Nebula: Arcadia sets off to meet the enemy.

A little leak will sink a great ship."Upon victory, Harlock orders First mate Yattaran to secure the hostages. But, Yattaran ends up being the one who is captured! Dr. Zero, who has known Yattaran since elementary school, proceeds to tell the crew about his rarely seen genius and ability to analyze the structure of the Arcadia. The Mazone, Elza, sent on an intelligence gather mission, decides to use Yattaran's love of models to get information on the structure of the Arcadia by challenging him to a model building contest. He is to build a scale-model of the Arcadia. But, right when he completes it, Harlock and the crew show up and Yattaran is recaptured.

Zol issued the attack order! Your father!"A surprising couple, Zorba, the son of the warrior Zol, and a Mazone medic named Lucia, escaped from the Mazone fleet. There are members in the crew who doubt Lucia and think she may be a spy, but when they see that the Mazone are truly trying to recovery the two, they begin to trust her. Then the Mazone launch their general attack. Zorba is upset over his mother's execution, but Harlock yells at him and he become brave again. He decides to use himself as a decoy to protect the Arcadia. The two of them are hit by the Mazone and they sparkle off almost like a shooting star.

This is a gamble. But it's a gamble we will win."Doctor Zero becomes extremely resentful over Zorba and Lucia's murder. So, he sets off to do battle in the midst of a magnetic storm and leaves his pet cat to the ship's cook, Masu-san. He leaves alone in a fighter. Then, with the cat who snuck into the cockpit when he wasn't looking, he prepares for death in a violent dogfight. Shortly after, Tadashi informs Harlock that the Mazone mothership he shot down was actually a passenger ship. The Mazone are not just plotting an invasion but are on a mass exodus in search of a new home!

You have awakened the lion that sleeps within me."Due to Harlock's unrelenting resistance, there is a growing resentment between the Mazone military and its civilians. There is a faction in the military saying the civilians are just a nuisance and should be cut off. But the queen has resigned herself to complete the exodus of all her peoples to Earth. When Tesius breaks away from the caravan with a group of Mazone, the queen sends her subordinate Cleo to deliver her punishment. She lets Tesius commit suicide rather than kill her...

Queen Lafresia is a Mazone with a heart."Having a hunch as to the reason why Harlock so staunchly opposes them, Queen Lafresia sends someone on a mission to Earth to find out why. They threaten Commander Kiruta and find out about Mayu. Finally believing the warnings about the Mazone that Harlock spoke of, Kiruta pleads to the Prime Minister to defend the Earth. But the Prime Minister does not deem the Mazone a threat. Kiruta finally understands Harlock's impatience with him. Then, after appearing in front of Harlock via hologram, Queen Lafresia is called a coward by Harlock. Then she makes up her mind to kidnap Mayu. She is taken away from Kiruta, who was protecting her, by a Mazone.

A man learns little by little while in battle."The Mazone come attacking the Arcadia which has had too much free time lately. Tadashi, thinking he may find clues to Mayu's whereabouts, gives chase in a fighter and is wrecked on the Rainbow Planet. A Mazone civilian saves him. Believing their story that they escaped in search of freedom, Tadashi befriends the girl, Kirika. Though he's hated the Mazone up until now, Tadashi gives a grass whistle to Kirika and they quickly grow close. But then he sees that it was all a trap to get close to him. He's saved by Harlock in the brink of time and grows due to this mistake.

If you can imagine, I drank whiskey that time..."While the Arcadia is being repaired at the dock of a Pirate Island, Tadashi and Tori-san come back with a pair of glasses. Harlock says they belonged to the man who built the Arcadia. Harlock met that man, Tochiro Oyama, in a bar in the Ulysses Nebula. The two of them got along great, but due to the influence of a mysterious woman named Emeralda, the two of them got a bad reputation and were sent off to the mines on Bad. The truth is Emeralda needed the help of the two men to rescue her younger brother Jimmy who was sent there already. After being freed from life in the mine, Tochiro and Emeralda got married and had Mayu.

We're all as one, together on the Arcadia."The Arcadia is rapidly being repaired on a Pirate Island while Lafresia continues her bloodthirsty hunt for it. While this is happening, Harlock tells Tadashi the secret story behind the Arcadia's origins. As fate would have it, Commander Kiruta captured and enlisted the services of a brilliant scientist named Tochiro to build a battleship to help capture Captain Harlock. However, Harlock saves Tochiro after he is in a pinch on Heavy Meldar, a planet which was being cultivated and they escape on the newly built Arcadia. Though it was a close call, they escape, but Tochiro (is hit with a bullet and) dies right after. Emeralda, wishing to remain with Tochiro, entrusts their daughter, Mayu, to Harlock. She then follows Tochiro out into space in a burial at space sea.

Earth is meaningless to me without Mayu."The Mazone plot to use Mayu to lure Harlock and the Arcadia to the Wind Planet and then attack with a powerful mine. As the Arcadia is making up its mind as to where they will go, they intercept a communication saying that the Mazone have sent advance troops to Earth. The crew asks Harlock if they can return to Earth. As Harlock is pondering what to do, the sound of Mayu's ocarina ominously comes to them from the Wind Planet, so they set their course to there. Thanks to the will of Tochiro, which remains on board the Arcadia, they are able to escape the Mazone's trap. Just as it looks like they will succeed in rescuing Mayu, she is whisked away to another planet.

When a man is searching for his final resting ground, don't go running your mouth."Commander Kiruta learns of the existence of the Mazone and persistently tries to inform the Prime Minister of the impending doom. Nevertheless, the Prime Minister ignores his pleas and begins to think of Kiruta as a dangerous person who may pull off a coup d'?tat. Then, Kiruta encounters Commander Otawara in a drinking establishment once again. He was the former commander who was accused of being a murderer after killing his wife upon finding out she was a Mazone. Learning of the Mazone invasion, Otawara leaves in a fighter all alone and makes contact with the Arcadia. He then leaves his final parting words to his former lover, whom he broke up with due to a misunderstanding, Masu-san. He then charges into the Mazone's crosshairs. Harlock is impressed with Otawara and vows once again to rescue Mayu.

It's time for our showdown, Lafresia."The Arcadia is trapped due to an artificial gravity device. However, they escape and protect Mayu from the Mazone base. However, she is suffering from post-traumatic stress disorder after being held captive for so long, and if she stops playing her ocarina, she goes into terrible bouts of terror. Worried that she'll die at this rate, Harlock turns to the main central computer which harbors her father, Tochiro's soul, in order to save her. Finally, after the computer plays her a lullaby, she is able to go to sleep.

Mayu, come here. The Earth is beautiful."After rescuing Mayu, all that remains is the final showdown with Lafresia. Harlock decides that she cannot remain on the ship during the battle and to return her to Earth. At the same time, Commander Kiruta, after pleading dozens of times regarding the impending Mazone invasion to the Prime Minister, is accused of treason due to a plot by his secretary, Shizuka Namino. Kiruta is slated to be executed the following morning and there is nothing more he can do. However, Shizuka saves him from this fate. In order to save Shizuka from the hands of the police, Kiruta turns to his one-time rival Harlock for assistance. He swallows his pride to Harlock as he promises to take her someplace safe. It turns out that this was what Shizuka wanted all along.

Even within all this silence, a flame is toiling."The beautiful, dazzling Shizuka Namino becomes a bit of a celebrity on board the Arcadia after being rescued. However, she's really a spy sent by Queen Lafresia. Upon the Queen's orders, she takes photos of the ship with a camera in her earring and seeks to discover Harlock's true intentions. However, Harlock doesn't fall to her sexual advances and provokes Lafresia, almost as if he knows Shizuka's true identity. Lafresia, hearing his words over her earring transmitter, becomes infuriated. She suddenly sends her main fleet out. At the same time, Shizuka realizes that the forty-second person on board the Arcadia is Tochiro Oyama.

It's cold in space."Upon realizing that Harlock knew who Shizuka's real identity is, she deems that she has failed in her mission. Harlock was going to banish her from his ship but he sees Shizuka help someone out and reconsiders. He decides to let her stay on the Arcadia but she then tries to blow up the main computer! Harlock scrambles to get the bomb out of the way and almost dies! The truth is that Shizuka was in love with Harlock, and as she couldn't live her life as a failure, she wanted to die by Harlock's doing.

Commander Kiruta gave me his word. I have trust in a man's promise."The invasion Mazone forces finally begin their attack on Earth. With no power to resist, the air space on Earth is quickly dominated. The Arcadia passes the main Mazone fleet by utilizing an electromagnetic storm and quickly rushes to Mayu's school to get her to safety. Kiruta says that the elder Hasshi who took care of him when he was young, in Egypt, would be able to look after her. Harlock agrees to entrust Mayu to Hasshi. As they make their way through the battle field to deliver Mayu to Egypt, Kiruta is injured. Nevertheless, they get the Arcadia to safety. It's there that Harlock tells Mayu the truth behind her father, the main computer.

Have a drink and talk to me. Sometimes people need to clear the air between them."The Arcadia leaves for space with Kiruta on board, after he was injured while trying to save Mayu. Before the final showdown, Kiruta confesses his true feelings to Harlock. About how he rescued a bunch of juvenile delinquents who were branded criminals, and how he wanted to create a future for them. He then drums up the courage to ferociously fight and closely battles with Mazone who board the ship. He then sacrifices himself to put up a defense and to protect Tadashi and First mate, Yattaran. Harlock buries him with respect.

I want to have a drink with you. Once the battle is ended."After a bunch of skirmishes, the true battle finally begins. The Mazone use an underhanded tactic by camouflaging a medic ship and sneaking in to attack. Harlock then rescues a pregnant woman from a civilian ship that they accidentally attack. As this is more important than being friend or foe, they ignore the Queen's orders for the time being. Neither party attacks until the baby is safely born. Seeing this side of Harlock for the first time, the Queen decides to stop the petty tricks and to fight Harlock directly.

I want to make a flower bloom. A flower of the future."Making its way past countless gunshots, the Arcadia finally arrives at Queen Lafresia's flagship. The crew sans First mate Yattaran makes a full assault on the ship. Harlock then confronts Queen Lafresia, who is wearing a battle uniform. They clash swords as she furiously battles the man who trying to crush her dream. Then, Harlock's friend who is in the Arcadia helps Harlock to victory. When Harlock sees the red blood flowing from Lafresia's veins, he decides to let her and the Mazone go. However, her final words are "I will leave”.

Mayu, plant flowers on this burnt field. Then call the butterflies and birds back here. Daiba, make history."Harlock and his crew go for their triumphant return to Earth, but, all that awaits them is an order that they've been banished from Earth. Harlock, thinking for the young crewmembers' sake, pleads to the Prime Minister to just pardon them and to disband as pirates. However, even that plea is rejected. At that moment, all the Mazone that were lying dormant on Earth arise. Harlock realizes that the Queen hinted at this happening but it was too late, cities are laid in ruin. The Prime Minister cries for help to Harlock and they decide to have their final fight for the sake of Earth. Peace is restored. Harlock entrusts the remnants of Earth to Tadashi and the gang and once again heads for space.