Mobile Suit Gundam Unicorn is set in the same timeline as the original Mobile Suit Gundam, but in a different story arc. The series follows Banagher Links, a seemingly normal boy living and going to school on the space colony Industrial 7. When he meets a mysterious girl named Audrey Burne, he is thrust into a new conflict between the Earth Federation and Neo Zeon, as well as being caught up in a secret surrounding Laplace's Box.
The story focuses on Banagher and his journey to uncover the truth behind Laplace's Box while also fighting against both factions of the war. Along his journey he will meet many allies and enemies alike, all of whom have their own agendas and secrets that could change the course of history. With powerful mobile suits on both sides of this conflict, it will be up to Banagher to save not only himself but also those around him from certain destruction.