Harlock is the latest descendant in a lineage of aerial warriors. His ancestors include Phantom F. Harlock I, an early 20th-century explorer who attempted to fly over New Guinea's Owen Stanley Mountains, and Phantom F. Harlock II, a German Luftwaffe pilot during World War II. The latter forged a pivotal bond with Japanese engineer Toshiro Oyama by helping him escape to Switzerland, culminating in a blood oath of eternal friendship between their families. This pact directly influences Harlock's destiny.
Returning to Earth as a Solar Federation officer in the late 30th century, Harlock finds his homeworld conquered by the Illumidus Empire and their Tokargan allies. The subjugated human population largely blames defenders like Harlock for failing to prevent the invasion. Amidst this oppression, he searches for Maya, his lover, who broadcasts clandestine messages of hope as "The Voice of Free Arcadia," symbolizing resistance. During a confrontation with Tokargan forces, Harlock suffers a gunshot wound to the face, losing his left eye – an injury that becomes a defining trait.
Harlock reunites with Tochiro Ōyama, Toshiro’s descendant, who reveals he secretly constructed the spaceship *Arcadia* as a tribute to the ancestral friendship and an embodiment of freedom. He also reconnects with fellow space captain Emeraldas, an old ally who joins his rebellion despite initial neutrality. In the ensuing battle, Tokargan allies sacrifice themselves to protect the *Arcadia* from the cosmic Flame Stream Prominence, analogous to the "Owen Stanley Witch" from his ancestor's ordeal. Maya is killed during the uprising. Though Harlock defeats Illumidus commander Zeda, Earth’s collaborationist leader, Triter, exiles him and his allies.
Rejecting an Earth that prefers subservience over freedom, Harlock adopts the identity of a space pirate, embracing the skull-and-crossbones flag as defiance. He departs aboard the *Arcadia* with Tochiro, Emeraldas, and a crew of idealists, vowing to live by his code: "I live in freedom under my flag." This transformation establishes his archetypal persona as a stoic, honor-bound loner fighting solely for his convictions. The number 42, frequently seen on his attire, alludes to the Japanese cultural symbolism for death ("shini"), reinforcing his fatalistic worldview.
Later media iterations continue his exile narrative, such as *Endless Orbit SSX* (1982) depicting the *Arcadia*'s quest for a cosmic sanctuary. Alternate continuities like *Harlock Saga* (1999) reimagine his youth during Earth’s conquest by godlike entities, retaining his core ethos. The 2013 film *Space Pirate Captain Harlock* recontextualizes his rebellion against a decaying Earth, while the manga *Captain Harlock: Dimensional Voyage* (2014) amalgamates elements from multiple Leiji Matsumoto works, with the *Arcadia of My Youth* origin remaining foundational to his identity.