Time Crisis 3 incorporates a new type of weapons system allowing the player to switch between the standard 9-round handgun, a fully automatic machine gun that can hold 200 rounds, a shotgun with 50 shells and a 5-round grenade launcher with powerful splash damage.

The game also refines the crisis flash system which life-threatening shots are brighter, making pedal-releasing advisories easier.

In 2003, 6 years after Time Crisis II, Astigos, the largest island in the Mediterranean nation of Lukano, is invaded by special forces from the neighboring Zagorian Federation.

Inside, she downloads intelligence that leads her to discover the Zagorians have acquired tactical ballistic missiles, which they intend to use to eliminate the rest of the LLF and potentially threaten neighboring nations.

Alicia transmits the info to her contact at the V.S.S.E., who in turn gets the agency to dispatch agents Alan Dunaway and Wesley Lambert to destroy the missiles.

Posing as fishermen, Alan and Wesley launch an attack on Marano Beach but are quickly cornered into a shipwreck by the Zagorian defenders.

Randy Garrett, the head of Zott's "Assassin Squad", leads them into an ambush, during which he destroys the bridge, causing the train to fall into the river.

Using her sniper skills, Alicia simultaneously destroys the detonator and kills Jake before sending the burning wreckage crashing into the sea.

Their mission a success, Alan and Wesley return home, while the LLF ultimately defeats the Zagorians and forces them out of Lukano, freeing Astigos Island.