Logan, known as Yama in the original Japanese release, is the narrative's central character. He originated on a Gaia Sanction colony on terraformed Mars, living with his older brother Ezra and childhood friend Nami. A childhood accident occurred when Logan tried restoring his deceased mother's flowers in a greenhouse, inadvertently causing an explosion that paralyzed Ezra and left Nami dependent on life support. This event burdened Logan with profound guilt, driving his actions to seek redemption. Ezra, now a high-ranking Gaia Sanction admiral, exploits Logan's guilt by assigning him a dangerous mission: infiltrate Captain Harlock's Arcadia to gather intelligence and assassinate Harlock. Logan accepts, hoping to atone for the past. Boarding the Arcadia, Logan initially maintains loyalty to Gaia Sanction while learning the crew's operations. He demonstrates natural aptitude with the ship's weaponry, particularly the mounted cannons, earning tentative acceptance despite friction with crew members like Kei Yuki. During a critical mission to plant a detonator device on a remote planet, Logan risks his life to save Kei from a fall, an act that begins shifting his perspective. Harlock later rescues Logan, revealing foreknowledge of the infiltration and offering Logan a place among the crew, appealing to his desire for true freedom. This prompts Logan to defect from Gaia Sanction and fully align with the Arcadia. Logan's allegiance faces a severe test upon the crew's return to the Solar System, confronting Ezra and the Gaia Sanction fleet. Ezra exposes Harlock's true plan: instead of restoring Earth, Harlock intends to detonate strategic warheads to destroy the current universe and trigger a new Big Bang. Reeling from this revelation and feeling betrayed, Logan switches sides again, helping Ezra capture the Arcadia and imprison its crew. This decision leads to tragedy. Ezra confronts Nami, discovering she provided Logan with classified information to aid the Arcadia. During their argument, Nami reveals she sacrificed herself to give Ezra peace, confessing her love for Logan before her life support fails. Ezra conceals the truth about Nami's death from Logan, claiming she died naturally. Consumed by grief and suspicion, Logan travels to Earth's surface, discovering a meadow of living flowers—fulfilling a dream once shared with Nami. This discovery proves Earth can sustain life, fundamentally altering his outlook. Armed with newfound hope, Logan frees the Arcadia crew and convinces Harlock to abandon the universe-destroying plan. Together, they expose Gaia Sanction's deception about Earth's condition. During the ensuing battle, Ezra boards the Arcadia and confronts Logan. Their zero-gravity fight culminates in Ezra shooting Logan in the face, leaving a scar similar to Harlock's. Harlock intervenes, mortally wounding Ezra. With his dying words, Ezra reveals diverting a superweapon blast was motivated by Nami's love for Earth's flowers. After the Arcadia crash-lands on Earth, Harlock entrusts Logan with the final detonator, offering him the choice to end the universe. Logan refuses, declaring Earth a "gift from Nami and Ezra." Accepting Harlock's symbolic eyepatch to cover his injured eye, Logan assumes command of the Arcadia and becomes the next Captain Harlock, tasked with preserving the myth of freedom for the universe.