In Universal Century 0079, Zeon intelligence has identified a prototype Federation Gundam under development in a Federation base in the Arctic. Elite Zeon MS commandos are dispatched to destroy the prototype, but before they can accomplish their mission the Gundam is launched into space. When the Gundam turns up in a Federation R&D base inside the neutral space colony Side 6, the Principality launches a covert operation to destroy the Gundam utilizing the commando team originally dispatched to assault the Arctic base, including young rookie Bernard "Bernie" Wiseman. However, the raid fails and the entire team is killed except for Bernie.

After crashing his mobile suit, Bernie manages to befriend Alfred "Al" Izuhura, an elementary school boy enamored with a romantic vision of warfare and excited by Bernie's status as a mobile suit pilot regardless of his allegiance, and Al's neighbor Christina "Chris" Mackenzie, secretly the Gundam test pilot. As Bernie tries to repair his damaged mobile suit while hiding out within the station, he develops a close friendship with Al and slowly becomes infatuated with Chris, both pilots remaining unaware of each other's true natures.

As time passes, Bernie discovers that Zeon will destroy Side 6 with a nuclear weapon if he cannot destroy the prototype Gundam. Feeling that he has no choice if the station is to be saved, Bernie takes his mobile suit and goes to engage the Gundam. Believing Side 6 to be under Zeon attack, Chris is ordered to pilot the Gundam in the station's defense, and she and Bernie engage in a destructive battle within the station. Al discovers that the Zeon ship carrying the nuclear weapons was captured, meaning Bernie has no more reason to fight. Alfred goes to try and stop Bernard, only to see Bernie's mobile suit destroyed and an injured Christina pulled from the heavily damaged Gundam.

Afterwards, Chris tells Al that she will be leaving Side 6, and asks Alfred to say goodbye to Bernard for her, still unaware that she had actually killed him. Al does not have the heart to tell her the truth and agrees to her request. The series closes with Al's school holding an assembly in which the principal talks about the effects of war. Al, remembering his time with Bernie, begins to weep uncontrollably during the speech. Al's friends, misunderstanding his grief, try to reassure him that another "cool" war is bound to happen soon.