The first game in the Front Mission series to take you to the African Continent. The year is 2034 and guerilla fighters are terrorizing local governments in Africa. You are charged with breaking these terrorist organizations with the WAWs (Walking Armored Wanzers) at your disposal.

Front Mission Alternative is a variation on the series' standard strategy theme in that you do not control the action, but direct it. You issue orders on a tactical map and your platoons of Wanzers carry them out on their own. Like other Front Mission titles, you can outfit your Wanzers with an assortment of weapons and equipment. Features over 30 missions and multiple endings.

Set in 2034, the story of Front Mission Alternative takes place in Africa. In the early 21st century, nations around the world form regional entities to combat a global recession and other crises. While many regions thrive under their newly formed supranational unions, the nations of Africa fall deeper into environmental, racial, and ethnic conflicts. In an attempt to help them, the European Community (EC) and the Oceania Cooperative Union (OCU) assisted the African countries in forming a continental alliance called the Organization of African Consolidation (OAC). Although it initially thrives in the first three years, disputes flare up between the OAC's five regional blocs - the Union of Northern African States (UNAS), the South African United States (SAUS), the Community of Central African States (CA), the East African Communities (EA), and the West African States Community Union (WA). Tensions rise and with diplomatic efforts failing, the nations go to war, leading to the outbreak of the African Conflict.

The plot of Front Mission Alternative revolves around the Independent Mobile Assault Company (IMAC), a special joint unit of soldiers from the OCU and the SAUS led by OCU Ground Defense Force 2nd Lt Earl McCoy. The SAUS government deploys the IMAC to stop the civil conflicts in its territory and in the other blocs. Piloting a new bipedal weapons platform called the wanderwagen or WAW, the IMAC successfully quells the violence across the continent. As they travel north to support the Western African Liberation Front, the company starts encountering unknown WAWs and WAW-vehicle hybrids known as "mobile weapons" being used by terrorist forces. The EC intervenes through the deployment of an elite anti-terrorism unit, but appear to be aiding the UNAS in prolonging the war. As the IMAC starts fighting their way into UNAS territory, they uncover connections between the terrorist uprisings, civil conflicts, the true cause of the war, and how the EC factors into the situation.