This movie is an alternative version of the TV series; it is composed of the two 2007 OVAs, edited to improve the pacing of the plot, and an extra segment akin to a TV episode where the cast are given the task of studying flowers. The plot has several differences to the TV series.

In a distant future there is an organization called Deava which had to fight against the so called "Shadow Angels", creatures that had survived for over 12,000 years whose only purpose was to destroy humanity. Apollo, a seemingly normal human, was in fact the reincarnation of a fallen Angel called Apollonius, who in turn had to fight against Touma, a Shadow Angel, along with his comrades in order to prevent the destruction of the Earth.

Onto their third serialization, manga duo Moritaka Mashiro and Akito Takagi—also known by their pen name, Muto Ashirogi—are ever closer to their dream of an anime adaption. However, the real challenge is only just beginning: if they are unable to compete with the artist Eiji Niizuma in the rankings within the span of six months, they will be canceled. To top it off, numerous rivals are close behind and declaring war. They don't even have enough time to spare thinking about an anime! In Bakuman. 3rd Season, Muto Ashirogi must find a way to stay atop the colossal mountain known as the Shounen Jack rankings. With new problems and new assistants, the pair continue to strive for their dream. [Written by MAL Rewrite]

An exoskeleton weapon engineered by Japan, Infinite Stratos (IS) can be piloted only by women. Its power and combat prowess are so immense that an international treaty has been signed banning its use as a military asset. When it is discovered that 15-year-old Ichika Orimura is the only male capable of steering an IS, he is forcibly enrolled in the Infinite Stratos Academy: an all-female boarding school, the students of which graduate to become IS pilots. At this training school, Ichika is reunited with two of his childhood friends, Houki Shinonono and Lingyin Huang, and befriends Cecilia Alcott, an IS representative from the United Kingdom. Guided by the legendary pilot Chifuyu Orimura—their strict homeroom teacher and Ichika's older sister—Ichika and the girls will need to use everything at their disposal to defend themselves and their academy against the dangers that will arise during the course of their thrilling school life. [Written by MAL Rewrite]