Kou Ichinomiya is the son of a wealthy businessman who holds a firm belief in his elite status. As such, he is determined to avoid becoming indebted to anyone; but one day, after a run-in with some mischievous kids on Arakawa Bridge, he ends up falling into the river running underneath. Luckily for him, a passerby is there to save him—but now, he owes his life to this stranger! Angered by this, Kou insists on paying her back, but this may just be the worst deal the arrogant businessman has ever made. The stranger—a stoic, tracksuit-wearing homeless girl known only as Nino—lives in a cardboard box under the bridge and wants only one thing: to fall in love. Asking Kou to be her boyfriend, he has no choice but to accept, forcing him to move out of his comfortable home and start a new life under the bridge!

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.

For thousands of years after its development, mankind used the written word for communication between people and generations. As millenia passed and technology became more prevalent, writing - and thus, communication as a whole - diminished, until it could only be found on cell phones and computer screens. Seeing an opportunity, the sorcerer Sogan Kenzaki starts infecting words with the Nesta Virus, which brings them to life and turns them into monsters called MJBK (Menace of Japanese with Biological Kinetic energy). To counter this attack against humanity, an organization known as DEAVA (Division of EArth Verbalism Ability) assembles a group of youths with the ability of Verbalism. They have to pilot the vector machines, which are used to form the mechas dubbed Aquarions. The one wild card in the situation is the self-dubbed savior, a young man who is the direct relative of a famous calligrapher, named Akira Kaibuki.

Four high school girls in uniforms walk silently on the barren earth. These girls are time travelers who had been sent 6000 years into the future, from their present in which the same day is endlessly repeated, in order to evade human extinction. They studied time travel in school, were examined by the aptitude test, and were sent to the future as told. What should they do now? They had no idea. The only thing they could take with them from the present was a light, toy-like cellphone. Of course, it receives no signal here. As the girls are walking, they see strange birds flying in the sky, and a discolored river in the distance. Then, one girl finds an abandoned house, and recognizes the name inscribed on the front gates.