In the year Universal Century 0096, three years after Char Aznable's failed attempt to force human migration into space, life continues in the colonies orbiting Earth. One such colony, at Side 4, is home to Banagher Links, a 16-year-old who lives a quiet life among his classmates. Audrey Burne, the last descendant of a great tyrannical family, takes it upon herself to steal the key to a mysterious device known as "Laplace's Box." It is said that the Box has the power to shape the course of the universe, and Audrey travels to Side 4 in an attempt to take it from its current holder and keep it from the Sleeves, the surviving remnant of Char Aznable's Neo-Zeon. In her search, she stumbles across Banagher and changes his life forever. When Side 4 comes under the attack of the Sleeves and its prolific fighters Marida Cruz and Full Frontal, Banagher takes control of the newly built Gundam Unicorn to defend his friends and protect the fate of humankind. [Written by MAL Rewrite]

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.

Yoshizou Yukawa is a passionate hot springs enthusiast—a hot springs hunter who was able to sniff out the source of springs. One day, while searching for a hidden hot spring to revitalize a town, he slips off a cliff and dies. He is then reincarnated into another world by an Inari deity of a small shrine hidden in the rocks. Yoshizou is joined by Inari's messenger princess, Mayudama. The hot spring hunter within Yoshizou is stirred right away, as he takes a bath with Mayudama in the hot spring he just discovered. Then, an elf girl appears...