
The VCPD Riot Squad is no match for the ECM's munitions, prompting Rage and Smarty to help the disadvantaged riot squad. Normal chapterīrand, a bank robber hired by the ECM, robs a large bank in downtown Virtua City. While the Virtua City police secured the pharmacy building, Janet receives disturbing information regarding about the pharmacy's genetic cloning system being missing. Proceeding deeper inside the pharmacy research lab, Rage and Smarty encounter a man named "Glitter," who is liable for the invasion. Throughout the pharmacy campaign, Rage and Smarty encounter a mysterious man known as "Gale," a ninja with unknown intentions. When the ECM took over a large pharmacy building, Rage and Smarty were ordered by the VCPD to apprehend the invaders and secure the building. The game follows the three characters as they investigate three crimes performed by Virtua City's new crime syndicate, the ECM.

Virtua Cop 3 allows the chapters to be played in any desired order. The newly designed gun used in the game is named the Guardian II, and was designed by Tokyo Marui, famous for their model guns. Like the previous installments, players progress through the game choosing between three missions which vary in difficulty. The alternative weapons include the Smith & Wesson Model 629, Benelli M4 Super 90, H&K MP7, and the H&K G36C. Virtua Cop 3 also allows players to toggle between different weapons by pressing a button on the gun instead of having to use just one weapon, as in previous entries in the series. The meter can be replenished by shooting more enemies. While in ES mode, time slows down as the player's ES meter is depleted.

Virtua Cop 3 introduces a new slow-motion " bullet time" mechanism called "ES mode" which allows players to slow down time by stepping on a special pedal. The game retains the same gameplay as its predecessor with players shooting onscreen enemies using a gun controller.
