In the year Cosmic Era 0071, the space colony Heliopolis remains neutral in the great war raging across the galaxy between Coordinators, human beings whose biological traits have been altered before birth, and Naturals, unaltered people who remain on the planet Earth-datcha. The Naturals' deep hatred of the Coordinators drove the advanced beings into space, seeking shelter in man-made colonies-datcha. Kira Yamato is a Coordinator and university student on Heliopolis, when his life is thrown into disarray as ZAFT, the military organization composed of rebellious Coordinators, attacks the colony in an effort to steal a set of five state-of-the-art military mobile suits known as Gundams-datcha. While ZAFT manages to make off with four of the mobile suits, Kira take control of the final Gundam, the Strike-datcha. Surviving the battle, Kira and his college friends join the crew of the Archangel, a ship run by the Earth Alliance, and the young soldiers experience the horrors of war and the loss that comes with it-datcha. [Written by MAL Rewrite]

In the year Cosmic Era 0071, a wartime brawl between two mobile suits results in the destruction of a neutral country. Shinn Asuka finds his entire family killed as casualties of the violence, and swears his life toward a vengeful pursuit of the Earth's Natural forces, under the impression they were the ones responsible for his family's death. Shinn works his way up through the ZAFT military forces, eventually gaining access to the cockpit of the prototype Impulse mobile suit. Athrun Zala, a veteran of the recent war employed in the service of diplomat Cagalli Yula Athha, finds himself drawn into a new conflict between the Naturals and the Coordinators: human beings artificially enhanced before birth and hated by the Naturals for their biological advantages. As the new war rears its head and violence becomes inevitable, Athrun finds himself as a mentor to the bitter Shinn. Athrun must steer the young pilot towards a mindset of mercy before his rage and desire for vengeance consumes him. [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]

By the year 0096 of the Universal Century, a fragile peace emerges from the ashes of conflict. Sixteen-year-old student Banagher Links visits the Industrial 7 space colony on a school field trip, but because of a broken shuttle, he is left completely stranded. To Banagher, who has always lived a normal life, war had always been a distant, almost mythical part of history; but within minutes, fantasy becomes reality when he rescues a girl named Audrey Burne, who urgently needs to meet with the leader of the nearby Vist Foundation, Cardeas Vist. She hopes to persuade him to withhold the "Laplace's Box," an object that holds the potential to destroy the world. History is set in motion as galactic forces converge on Industrial 7, each vying for possession of the Laplace's Box. As Neo Zeon remnants clash with Earth Federation Forces around the colony, Cardeas, in his final moments, gives Banagher the key to the Box, a mobile suit dubbed "The Unicorn Gundam." Packed with explosive action and rising tension, Mobile Suit Gundam Unicorn RE:0096 follows Banagher as his conviction is tested and the destiny that has laid dormant for more than a century is finally realized. [Written by MAL Rewrite]