The year is 102014. The Earth's surface lay in ruins, no longer able to sustain human life. As such, humans have retreated underground and created civilization within cities known as Panopticons. Hope remains within the human race that they will one day be able to return to the surface, but for now, a new system to accommodate underground living has been established: Panopticons offer safety in exchange for service. Unfortunately, inequality between population and resources proves problematic; even newborns are considered criminals due to their consumption of valuable resources. The player assumes the role of a customizable male or female citizen faced with a sentence of 1,000,000 years for the crime of living. The player character must attempt to diminish their sentence by performing as a volunteer in war, primarily against monsters referred to as "Abductors" which are generally known to capture ordinary civilians. The player character is supposedly resigned to this unpleasant life until a chance meeting with Beatrice, a woman who comes from a mysterious city in the sky.
Freedom Wars is a third-person action game with an emphasis on combat. The player can switch between guns and swords in battle, and also has the ability to use their "thorn", a grappling whip which allows them faster travel and extra combat options. In battle, the player always has the assistance of their Accessory, an android who, like the player character, is fully-customizable. Players can order their Accessories to fight alongside them or rescue civilians from the battlefield. Missions usually consist of fighting against Abductors, but also vary between item retrieval and capture the flag-type objectives. Successfully clearing missions reduces the player's sentence, giving them more freedom and privileges such as more customization options and weapons. Online modes also exist, with competitive and cooperative modes for up to eight players. For competitive modes, players select a Panopticon to represent based on real-life cities and war with players in other regions.