Three years after the Belkan War, the Osean Federation and the Union of Yuktobanian Republics continued to place themselves as the greatest superpowers in the world. On the day of the treaty's signing, moderate extremists launched a coup d'état across the entire continent, fearing the presence of the Osean military and the withdraw of their mining rights.
As a last-ditch effort, Allied Forces HQ initiated Operation Fighter's Honor, in which they contracted the Scarface Squadron to assist in and spearhead an assault to tip the war back in the Allied Forces' favor.
Before each mission, the player can select which aircraft and special munitions to fly with, as well as which wingman to fly alongside the player. Two new mechanics introduced in Assault Horizon Legacy are known as Attack Maneuvers and Evasive Maneuvers. These are not to be confused with Dogfight Mode, which is used in Assault Horizon.
Attack Maneuvers require the player to stay very close to an enemy plane to fill up the AM Gauge. When the gauge is full, the player can press the Y button to allow the game to move the aircraft behind the enemy plane. Evasive Maneuvers evade incoming missiles from any direction. The player must press the Y button while moving the Circle Pad left or right to evade a missile that is closing in.