The Balamb Garden Revolt takes place in the Balamb Garden between forces loyal to Headmaster Cid Kramer and forces loyal to NORG. The brief conflict, which stems from a disagreement on how to handle the Garden's missile crisis, sees the ouster of NORG from the Garden.
SeeD and Galbadian top military official Fury Caraway join forces to assassinate Sorceress Edea in Deling City. The attempt is unsuccessful, and the SeeD members involved in the plot are imprisoned in the D-District Prison. Irvine Kinneas, the sniper from G-Garden assigned to assist the SeeD group, avoids capture and helps the SeeD escape. Squall Leonhart, the group's leader, chooses two party members to take with him to make their way back to Balamb Garden to warn the headmaster of the impending threat of Galbadian missiles of which they had learned of during their captivity.
As a response to the assassination attempt, Edea orders missile attacks on the Balamb and Trabia Gardens. Selphie Tilmitt's SeeD group fails to prevent the destruction of the latter, while Squall's party rushes to Balamb Garden to warn everyone to evacuate.
Seeking to save the Garden from the sorceress's wrath, NORG wants to apologize to her and frame the SeeD members involved in the plot as rogues. To prove his sincerity, he wants to hand over the members to Edea. Cid, realizing SeeD is facing the battle it was founded for, believes it should stand up for its original purpose and fight the sorceress.
Balamb Garden is divided into two factions, and the resulting war leaves it in chaos. Headmaster Cid's SeeDs prevail and the war ends as the Garden avoids Edea's missile attack by Squall's party restarting its ancient Centra machinery, morphing the building into a mobile form and narrowly escaping in time by moving the Garden away from the spot the missiles were programmed to target. The navigation systems lacking maintenance, the Garden flies astray into the ocean where it stays adrift.
Cid and NORG remain in disagreement. NORG, feeling a sense of ownership of the Garden, being its financier, attacks the SeeDs involved in the assassination attempt, planning to hand them over with or without support from the Garden. Upon defeat he closes himself away, ending the conflict.
Cid remains in charge of the Garden and NORG's Garden Faculty disappear from Balamb Garden. The Garden's B3 floor remains empty bar the strange cocoon that forms on the site NORG was defeated in. If the party did not save the boy in a blue shirt in the Training Center, he also disappears from the Garden and a girl dressed in red inherits his Triple Triad deck.