Taking place several years after the events in the original Kite film, Kite Liberator starts off with crew members of ISS along with Kōichi Doi, a food formulation researcher at Defy Foods, returning back to the Space Station on a Kudryavka shuttle. Doi had been researching various methods of preserving bone mass in zero gravity conditions, leading to healthy but frequently unappetizing food. While some members of the crew voice their distaste, the mission leader Orudo Noguchi reminds them of the necessity and benefits of the space foods. However, when it is found that Noguchi and another crew member have space radiation exposure and abnormally increased bone volume during a periodic medical check-up, Doi strangely questions the safety of his food, hinting that there may be more going on that is apparent. The two men are ordered by the doctor to discontinue any further missions to prevent further radiation exposure. In his room, Noguchi observes pictures of Monaka, his only daughter and gives Doi a small package to deliver to her.

Meanwhile in Tokyo during night time, two police officers pursue a violent pedophile through the streets and into a train station. The criminal enters a women's washroom and takes a young girl hostage after shooting two bystanders. The officers attempt to defuse the situation but are rebuffed with gunfire. The criminal forces the young girl into a stall, with the intention of fondling/raping her. However, the lights go out and the criminal is attacked and killed by the "Angel of Death", a female assassin. Hearing gunfire, the officers enter but find only the assassin's calling card: a flurry of white feathers on the dead suspect. Escaping the station on an outbound train after changing clothes, it is revealed that the "Angel of Death" is none other than Monaka Noguchi.