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]

In Universal Century 0088, the Anti-Earth Union Group (AEUG) has emerged victorious in its war with the Earth Federation's Titans at the cost of devastating losses. Neo-Zeon, the third faction in the war formerly known as Axis Zeon, remains as powerful as ever. Led by Newtype Haman Karn, Neo-Zeon has been implementing plans to take over both Earth and the space colonies. The AEUG flagship Argama heads to the Side 1 colony Shangri-La for repairs. Living in the colony is Judau Ashta, a 14-year-old junk dealer who is struggling to make enough money to put his younger sister through school. Upon the discovery of an escape pod containing a former Titans pilot, Judau and his friends are quickly led to the Argama in hopes of stealing a mobile suit which they can sell for a fortune. However, with the arrival of a Neo-Zeon ship seeking to defeat the Argama, Judau and his friends are dragged into to a conflict that will bring them across space and Earth. [Written by MAL Rewrite]