Misao Mitsuishi is the scientist responsible for overseeing Ai's training and development as the military's secret weapon against the M34 virus. Her duties include monitoring Ai's psychological state and preparing her abilities for deployment against infected threats. During this process, she forms a maternal bond with Ai, a stark contrast to the project's clinical objectives. This bond deepens as Misao learns of Ai's history of psychological manipulation and enforced isolation, including the removal of a pet dog that provided companionship due to its perceived interference with power development.

Misao becomes aware of Ai's profound loneliness within the restricted environment and acts as her confidante regarding these emotional struggles. When Ai forms a connection with Yuuji Tamiya, a NOA soldier, Misao witnesses the positive impact of this relationship on Ai's well-being. Following the military's decision to restrict Ai's contact with Yuuji, Misao facilitates their temporary escape from the facility, supporting their brief attempt to flee the project's constraints. These actions reflect her internal conflict between scientific duties and protective instincts toward Ai.

Throughout the series, she serves as a primary source of exposition regarding Ai's background, the nature of the experiments conducted on her, and the emotional costs of her isolation. Her knowledge encompasses the extent of Ai's sacrifices and the manipulation she endured under military necessity. Her portrayal is confined to the original ONA series, with no appearance or development in other official media such as spin-offs, movies, or additional seasons.