Captain Kobayashi commands the generational seed ship *Sidonia*, protecting humanity's remnants as they flee the alien Gauna. She is among the few surviving original crew members who defeated a Gauna over 600 years prior to the main events, having undergone biological treatments that granted her immortality. Her rank is marked by a distinctive mask worn during official duties, hiding her youthful appearance despite her advanced age. As a founding member of the Immortal Ship Committee, she directs *Sidonia*'s mission to reach a habitable star system. The committee initially consisted of essential personnel granted immortality to secure the ship’s voyage. Over centuries, it expanded to 25 members, with many growing corrupt and prioritizing political influence over survival. Roughly 100 years before the main events, Kobayashi executed dissenting committee members who opposed her leadership, consolidating authority to refocus on humanity’s preservation. Only six immortals remained active afterward, including Kobayashi, Hiroki Saito, and Lala Hiyama. Kobayashi employs a stoic, pragmatic leadership style, sacrificing personnel or ship sections if essential for humanity’s survival. She maintains emotional detachment during crises but occasionally blends anonymously into the crew in disguises like a nurse or restaurant clerk—one of her few personal indulgences. Her relationship with fellow immortal and legendary pilot Hiroki Saito, once close, fractured when she forcibly extended his immortality against his wishes. After Saito’s death, she became legal guardian to his clone, Nagate Tanikaze, partly out of sympathy but also to harness his loyalty and piloting skills for *Sidonia*’s defense. During Gauna conflicts, Kobayashi deploys resources strategically, notably assigning Nagate advanced Guardian mecha such as the Type-17 Tsugumori. Her decisions prioritize military efficacy over individual welfare, including abandoning pilots mid-battle or authorizing hazardous experimental technology. After colonizing the Lem star system, she remains aboard *Sidonia* as it departs to seek new habitable worlds, underscoring her commitment to humanity’s expansion. A continuity note clarifies that although she predates genetic modifications enabling photosynthesis in *Sidonia*’s populace, her full-body immersion during bathing scenes may imply a brain transplant into a photosynthetic clone body.