The game is set in the year 2171, 50 years after the events of Front Mission 5: Scars of the War. During the 22nd century, the world's superpowers look towards space for expansion and began constructing large structures called orbital elevators. With an increasing number of surveillance satellites and space-based technologies being developed, a Cold War-style atmosphere sets in as the supranational unions used these technologies to watch over their adversaries on Earth.

The plot of Front Mission Evolved revolves around USN engineer Dylan Ramsey. As an engineer for the weapons developer Diable Avionics, Dylan begins testing of a prototype wanzer on Long Island, New York. In the midst of the wanzer test, unknown forces begin attacking New York City and its orbital elevator, Percival. Worried about his father's safety in the city, he sets off for New York City inside the prototype. As he travels through the city to reach the National Strategic Research Laboratory (NSRL), Ramsey assists USN forces battling the unknown assailants. After battling through numerous enemy wanzers, vehicles, and aircraft, Dylan makes it to the NSRL premises just as missiles are launched into the building. With his father seemingly dead, he engages the attacker, Marcus Seligman of the Apollo's Chariot. The fight is cut short when the orbital elevator begins crashing down on New York City. After Percival collapses, Dylan is recruited into the USN Army as it prepares for war against the Oceania Cooperative Union.