Dr. Kenzou Tenma, an elite neurosurgeon recently engaged to his hospital director's daughter, is well on his way to ascending the hospital hierarchy. That is until one night, a seemingly small event changes Dr. Tenma's life forever. While preparing to perform surgery on someone, he gets a call from the hospital director telling him to switch patients and instead perform life-saving brain surgery on a famous performer. His fellow doctors, fiancée, and the hospital director applaud his accomplishment; but because of the switch, a poor immigrant worker is dead, causing Dr. Tenma to have a crisis of conscience. So when a similar situation arises, Dr. Tenma stands his ground and chooses to perform surgery on the young boy Johan Liebert instead of the town's mayor. Unfortunately, this choice leads to serious ramifications for Dr. Tenma—losing his social standing being one of them. However, with the mysterious death of the director and two other doctors, Dr. Tenma's position is restored. With no evidence to convict him, he is released and goes on to attain the position of hospital director. Nine years later when Dr. Tenma saves the life of a criminal, his past comes back to haunt him—once again, he comes face to face with the monster he operated on. He must now embark on a quest of pursuit to make amends for the havoc spread by the one he saved. [Written by MAL Rewrite]

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.