Kobayashi is the commander of the generation ship Sidonia, officially designated the twenty-eighth captain. She is one of the few remaining humans who directly survived the first war against the alien Gauna over six hundred years prior, an event that led to her becoming a member of the Immortal Ship Committee and gaining biological immortality. She almost always appears wearing a mask, a practice she maintains to conceal her ageless, youthful features and to hide her emotions from her subordinates, preserving an air of mystery and authority.

In the past, Kobayashi served as a Garde pilot, fighting alongside Nagate Tanikaze's grandfather. This history informs her personal interest in Nagate after he emerges from the under-dweller levels and becomes a pilot. She is unwaveringly committed to the survival of Sidonia and the last remnants of humanity. For much of the story, her authority is tempered by the Immortal Ship Committee, which demands she assign Nagate to highly dangerous, repeated missions despite her own concern for his well-being.

Her personality is defined by a cold, calculating pragmatism. She is decisive and rarely reveals her private thoughts, a trait reinforced by her masked public persona. Despite her stern exterior, she possesses a deep-seated empathy, though she consistently prioritizes the greater good of humanity over individual lives. Her primary motivation is the total annihilation of the Gauna threat.

Kobayashi's role is that of the supreme military commander, overseeing the deployment of Garde units and dictating Sidonia's strategic direction. Her most significant character development occurs during the Battle for Planet Nine arc. After a near-fatal collision with a massive Gauna results in severe casualties, she undergoes a profound shift in her leadership. Seizing full political power, she abandons a purely defensive posture for an aggressive offensive campaign to eradicate the Gauna from the Lem system. To achieve this, she authorizes the creation of Tsumugi Shiraui, the first human-Gauna chimera, demonstrating her willingness to push ethical boundaries for victory. She also secretly pursues the development of a highly dangerous experimental weapon that could destroy Sidonia itself if uncontrolled.

Her key relationships are shaped by her command position. She shares a unique bond with Nagate, viewing him as a vital asset and a living link to her past as a pilot, while feeling constrained by duty regarding his deployment. She oversees the development and deployment of Tsumugi, regarding the chimera as a necessary tool for humanity's survival. Ultimately, she clashes with and overcomes the Immortal Ship Committee to enact her total war strategy.

Kobayashi's notable abilities include the biological immortality granted by the Ship Committee, and her extensive experience as a former Garde pilot gives her a deep, practical understanding of combat strategy. Her greatest strength, however, is her unwavering resolve and her capacity to make the brutally difficult decisions required to navigate humanity through its existential crisis.