In the year 432 AC (After Calamity), a multinational order known as the Pacific Federation has control over the Cordium deposits across the Ring of Fire. In recent years, tensions between Federation member states have escalated to the point where the Cascadian Republic (a member state located in North America) declares independence and starts an armed rebellion.
Several private military companies such as the Sicario Mercenary Corps are hired by Cascadia in their war against the Federation.
The players control the game's silent protagonist simply known by his callsign "Monarch", who is a member of the "Hitman" team of Cascadian pilots employed by Sicario, which also include two other pilots (callsigns "Diplomat" and "Comic") and Monarch's weapon systems officer, callsign "President".
Other members of Sicario include "Galaxy", Sicario's primary AWACS operator, and the company's president, callsign "Kaiser", who is also a pilot and leader of the "Assassin" team.
After finishing their contract with the Creole Republic, the Sicario Maercenary Corps is hired by the Cascadian Republic in their war of independence against the Pacific Federation.
The Federation forces gain the upper hand in the early stages of the war, to the point of capturing the Cascadian capital city of Presidia; but by the efforts of Sicario (led by Hitman Team), the Cascadians turn the tide and reclaim most of the country's territory while surviving two encounters with the elite Crimson Squadron, composed of the Federation's top aces.
Hitman's immense combat effectiveness results in its pilots, especially Monarch, gaining notoriety amongst Federation and Cascadian forces alike.
During the course of the war, Hitman runs a mission on an offshore Federation-controlled research facility to uncover intel on their projects. However, Frost, a rogue mercenary from a prior war in Oceania, pilots an experimental superfighter from Icarus Armory's titular "Project Wingman" in an effort to stop the mercenaries; she is defeated, but survives with the combat data retrieved by Federation scientists.
During a subsequent mission to liberate Prospero, Cascadia's main economic hub, the Federation bombards the city with Cordium-enriched cruise missiles in an attempt to regain their control over the battle.
The warheads trigger an underground Cordium chain reaction that destabilizes the Ring of Fire, ravaging most of the Pacific Rim in resulting tectonic event. With the country in ruins and their sensors damaged, Hitman withdraws from the battle.
They re-encounter Frost, who is now leading a group of bounty hunters intent on eliminating Hitman. Hitman learns that their true identities have been leaked to the public, which compromise their safety as mercenaries.
They eventually shoot down Frost and the bounty hunters for good before reconnecting with the remnants of Sicario. As they plan on moving out of Cascadia, the Cascadian government offers Sicario a deal to keep them fighting.
Accepting the deal from the Cascadians, Sicario leads the rebels against the remaining Federation forces in the country, eventually defeating Crimson Squadron in a third and decisive encounter, while Kaiser assembles an army of mercenaries from across the world using some massive resources provided by the Cascadian government.
During the last major battle of the war to liberate Presidia, both sides of the conflict agree to a ceasefire as the battle winds down. However, Crimson 1, now overcome with madness from having to fight against his countrymen and losing his squadron, flies the Project Wingman fighter and attacks Presidia with Cordium missiles against his superiors' orders, causing widespread destruction and shooting down all pilots except for Monarch, whom he challenges to a duel.
Both the surviving Federation and Cascadian forces watch the battle with Sicario rescuing Monarch's wingmen. Crimson 1 is ultimately shot down by Monarch, ending the war.
Log files containing the game's lore reveal that after the war, Cascadia held up their part of the bargain with Sicario. Hitman's whereabouts are unknown, though it is implied that they used Cascadia's reward money to assume new identities, and the Cascadian government urges its citizens to report any information on the members of Hitman Team to the police.
Having suffered irreplaceably high casualties, and with their reputation irreversibly soiled by the use of Cordium weapons of mass destruction, the Federation faces multiple insurgent movements from other member states, backed by the now-independent Cascadia (which became a haven for mercenaries) among other foreign powers.