In the year Universal Century 0079, humans have colonized the area of space lying in between the Earth and the moon. However, the ambitious Zabi family, rulers of the Duchy of Zeon, the grouping of colonies furthest from the earth, has sparked a war.

After surviving attacks by Zeon's Char Aznable and Garma Zabi, the crew of Federation warship White Base and its mobile suits must battle Zeon forces through Asia, Europe, and the Atlantic Ocean if they are to reach Earth Federation's headquarters alive. During that process, many of its crewmembers must overcome their fears, losses, immaturities, and insecurities in order to persevere.

Amuro Ray and the rest of the White Base crew, now denominated the 13th Autonomous Corps, return to outer space to support the rest of the Earth Federation forces for the decisive battle against the Principality of Zeon's forces.

In UC 0093, the Federation has recovered from its defeat and has created a new anti-colonial special forces unit to deal with rebel forces: Londo Bell. Elsewhere in space, Char Aznable reappears out of self-imposed hiding with a declaration that he now commands his own Neo-Zeon movement, and intends to force the emigration of Earth's inhabitants to space by bringing about an apocalypse.