Maki Kitaki is the Prime Minister in the world of FLCL Alternative. She is an adult figure in a position of significant political power, placing her at a level above the teenage protagonists and their immediate concerns. Her personality is characterized by a pragmatic and dismissive attitude, especially when faced with large-scale, catastrophic problems. Upon learning of Medical Mechanica's plan to activate giant irons across the Earth, a process that would flatten the planet, she shows little concern for the impending global destruction. Instead of focusing on saving the world, her primary motivation becomes self-preservation and escape. She decides to leave Earth behind entirely, prioritizing her own survival over the fate of humanity.

Throughout the story, Kitaki serves as a figure of high-level authority who is aware of the monumental threat posed by Medical Mechanica. Her actions influence the overall plot by establishing a trajectory for some of the human characters. She works alongside Tsukata Kanda, a fellow adult who is also investigating the strange pins appearing around the city. In secret meetings, they discuss Medical Mechanica's plans, with Kitaki hinting at her own undisclosed intentions, which unsettle Kanda. Her decision to depart from Earth creates a scenario where other characters must find alternative solutions, such as Kanda's plan to use NO powers to transport people to Mars. Her key relationships are primarily with other adult characters, most notably her secretive partnership with Kanda. Her role contrasts with that of Haruko Haruhara, whom Kitaki refers to dismissively as a "being called Haru-something," instructing Kanda to deal with her. While the story focuses on the emotional growth of the younger girls, Kitaki represents the adult world's cynical response to a crisis: a retreat from responsibility. She does not demonstrate any notable supernatural abilities; her power is derived from her political office and the authority it grants her.