Learning that the Zagorian forces have set up a base in the abandoned Astigos State Observatory, Daniel and his lieutenant Jake Hernandez lead a small force to infiltrate and destroy it. Meanwhile, the surviving Lukano defenders organize themselves into the Lukano Liberation Force under Daniel Winston. Led by dictator General Giorgio Zott, the invaders conquer 80% of Astigos in a matter of weeks despite international protests. 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. As with the PlayStation 2 version of Time Crisis II, players can access the Crisis Mission exercise menu through prolonged gameplay. Unlike Time Crisis and Time Crisis II, the home console port features plot elements, features, and weapons not found in its arcade counterpart. Gameplay for Alicia is, for the most part, the same as the regular campaign, with occasional sections in which the player must use a Sniper Rifle to deal with enemy snipers. This title was later released for the PlayStation 2, together with a side story featuring Alicia Winston as a player, who is only an unplayable supporter in the arcade version of the game. The game also refines the crisis flash system which life-threatening shots are brighter, making pedal-releasing advisories easier.

This feature was later used in the port of Crisis Zone, with some changes. Only the handgun has unlimited ammunition, though players can shoot yellow-clad soldiers to gain ammunition for their other weapons.

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.

Time crisis 3 split screen