Midori Isami is a scientist and a key figure within the Orphan organization, the alien spacecraft at the center of the story. She is the wife of Kensaku Isami and works as his assistant in their research on organic energy and the revival of Orphan. Her marriage to Kensaku is not rooted in affection; she entered into it primarily to advance her own scientific ambitions and to secure a position of power within Orphan's hierarchy. Cold and calculating by nature, she is willing to manipulate those around her, including her own children, Yuu Isami and Quincy Issa, treating them as tools to further her goals rather than as family members deserving of care. She shows little maternal concern and often prioritizes her research over their wellbeing, a pattern that contributes to the deep fractures within the Isami family.

Midori's motivations are driven by a desire for control and recognition. Having lost her own father at a young age, she grew into a pragmatic and opportunistic woman who uses relationships to climb the ranks. She supports her husband's work on Orphan but also harbors contempt for his single-minded obsession. This lack of genuine connection leads her to seek personal fulfillment elsewhere, and she engages in an extramarital affair with Jonathan Glenn, a Reclaimer pilot, whom she fancies more than her husband. Her role in the story is that of an antagonist within the scientific and political backbone of Orphan, directly opposing the protagonists' efforts to prevent Orphan's catastrophic awakening. She is largely indifferent to the broader destruction that Orphan's revival would cause, focusing instead on the potential breakthroughs and influence it offers.

Key relationships include her strained ties with her daughter Quincy Issa, who becomes a Reclaimer commander, and her son Yuu Isami, who defects from Orphan. Both children grew up neglected by her, and this neglect fuels their later conflicts with her and the Orphan cause. Her relationship with her mother, Naoko Isami, is also marked by exploitation, as Midori uses her for childcare without hesitation. In terms of development, Midori remains largely static throughout the series, never redeeming herself or changing her self-serving outlook. Her notable abilities lie in her scientific expertise, particularly in organic energy theory and the operation of Orphan's systems, and her political acumen in maneuvering within the organization's leadership. She is a pragmatic and manipulative figure whose actions underscore the dysfunctional dynamics at the heart of the Isami family and the Orphan project.