In the future, with Earth's population rapidly increasing, humanity has developed giant orbiting space colonies gathered in clusters known as Sides. As the elites on Earth force most of the populace into space, rebellion begins to brew. In the year Universal Century 0079, one of the colony clusters known as Side 3 declares itself the Principality of Zeon and launches a war of independence against the Earth Federation. Despite having only a fraction of the resources of the Federation, Zeon quickly gains the upper hand in the conflict through the use of giant humanoid robots called mobile suits. Chief among Zeon's mobile suit ace pilots is Char Aznable, a mysterious masked man known as the Red Comet. When Char's squadron comes across the Federation developing its own prototype mobile suit called Gundam in the colony Side 7, his men launch a brutal attack. Amuro Ray, the son of the prototype's developer, gets in the Gundam and is able to fend off the Zeon attack. As Amuro soon finds himself directly in conflict with Char, he is forced to flee the colony on a Federation ship.

Alfred Izuruha is a 10-year-old who lives in the neutral colony cluster of Side 6 and, like most boys his age, is obsessed with the war between the Earth Federation and the Principality of Zeon. Unbeknownst to him, Al's next-door neighbor, Christina, is the test pilot of a prototype Gundam being developed in secret by the Earth Federation in the colony. A Zeon Special Forces team is assembled and tasked with infiltrating the colony in order to either steal or destroy it. When a skirmish breaks out between the Federation and infiltrating Zeon forces, the fascinated Alfred stumbles upon a Zaku mobile suit that has been shot down, piloted by Zeon rookie Bernard Bernie Wiseman. After this encounter, the two start a mutual friendship, so Alfred can learn more about the war that interests him so much, and Bernie can acquire inside information about the colony to aid his team's mission.

Over three hundred years have passed since the Calamity War, the great conflict between Earth and its outer space colonies. Now Earth is ruled over by four economic blocs, and the military organization Gjallarhorn is responsible for keeping the peace. Mars, on the other hand, depends heavily on Earth's economy. Horrified by the appalling living conditions that Mars' inhabitants have to bear, Kudelia Aina Bernstein, a young aristocrat from the Chryse Autonomous Region, gets involved in the Red Planet's independence movement. She hires the services of a local company, Chryse Guard Security (CGS), to escort her on the journey to Earth to negotiate economic conditions with the earthly bloc that controls the region. The Third Army Division—consisting of Mikazuki Augus, Orga Itsuka, and many other child soldiers—are chosen to protect her. When Gjallarhorn attacks the CGS facilities to assassinate the young revolutionary threatening their interests, Orga and his comrades must not let the attackers accomplish their goal—in fact, Gjallarhorn's actions might turn out to be the unintentional catalyst that leads the children to be the forgers of their own destiny.

Mayfly reveals Cima's backstory in flashbacks as she reflects on her past prior to the events of Episode 13. It reveals that Cima and her unit poisoned a Side 5 colony using G-3 nerve gas, under orders, but were treated as pariahs afterwards by their own countrymen for committing such an atrocity. At the end of the war her superior refused to let her retreat to Axis. Because their home colony Mahal had been converted into a weapon, Cima and her men were left stranded and homeless. (Source: Wikipedia)