Even with the Truce in place, the Matrix is by no means a safe environment. Once you jack in, you'll run into dangerous Exile gangs, redpills working for other Organizations, and various enemies whose goals oppose your own. While negotiation is sometimes an option, more often than not you'll have to defeat them in combat.

A hallmark of the Matrix movies is the intense combat styles used while jacked in. The Matrix Online reproduces these battles with a technology unique to the MMO world called “the Interlock Combat System”. There's nothing quite like going hand-to-hand (or gun-to-gun) versus an opponent in the wire-fu style of the Matrix movies.

Along with melee combat, there are Disciplines dedicated to the art of ranged combat. This includes both characters that learn to use high-power ranged weapons and those who learn to launch programs while in the Matrix in order to help or harm others.