"Mobile Suit Gundam 0079" is set in the Universal Century timeline, a future where humanity has colonized space. The Earth Federation and the Principality of Zeon are engaged in a brutal war for independence and control. The story begins with the Zeon forces attacking Side 7, a neutral space colony, to destroy a prototype mobile suit developed by the Earth Federation. Amuro Ray, a young civilian, accidentally pilots the RX-78-2 Gundam, a powerful mobile suit, to defend his home. This act thrusts him into the conflict as a key figure in the Federation's war effort.

Amuro joins the crew of the Federation's White Base, a prototype warship carrying refugees and military personnel. The ship is commanded by Bright Noa, a young but capable officer, and includes a diverse crew, such as the experienced pilot Sayla Mass, who has a mysterious connection to the Zeon leadership. As the White Base travels to Earth, it becomes a target for Zeon forces, particularly Char Aznable, a skilled and enigmatic Zeon pilot known as the "Red Comet." Char's rivalry with Amuro becomes a central dynamic, as both pilots push the limits of their abilities and machines.

The war escalates as the White Base faces numerous battles across Earth and space, showcasing the devastating impact of the conflict on civilians and soldiers alike. Amuro struggles with the psychological toll of combat and the burden of being a Newtype, a term used to describe individuals with heightened spatial awareness and empathy, believed to represent the next stage of human evolution. This theme is further explored through characters like Lalah Sune, a Newtype working for Zeon, who becomes a tragic figure caught between Amuro and Char.

The narrative delves into the political and ideological motivations of both factions. The Earth Federation is portrayed as a bureaucratic and often corrupt entity, while Zeon, led by the Zabi family, seeks independence but is plagued by internal power struggles and authoritarianism. The Zabi family's ambitions and rivalries drive much of Zeon's actions, culminating in a climactic confrontation at the Zeon stronghold of A Baoa Qu.

The series concludes with a decisive battle that sees the deaths of key figures on both sides, including Lalah and several members of the Zabi family. Amuro and Char's final duel underscores the personal and ideological conflicts that define the war. The Federation emerges victorious, but the cost of the conflict is immense, leaving the future of humanity uncertain. "Mobile Suit Gundam 0079" is a foundational work in the mecha genre, blending intense action with complex characters and themes of war, evolution, and morality.