No matter what people might have thought of the movies, there are few franchises that are as logical for an MMO setting as The Matrix. Human beings are running in a computer-generated world, granted super abilities, and each with their own political agenda. The Matrix Online takes place right after the third movie ends, where there is a tenuous peace between the Machines and the humans of Zion. There is a third faction to mix things up: The Exiles, who are rogue sentient programs who seek to protect their living space and influence in the Matrix. Players are called "red pills", who initially work for Zion but may later choose to work for any other faction. Currently, there is very little difference in being part of any given faction. The missions all tend to work out the same way.

The game is very high in style, and goes to great length to stick to what the movies have already established. "Jacking in," thrusts the player into a green world with streaming code that eventually shifts into a recognizable reality. While this is impressive at first, it can quickly become bothersome, especially if something attacks you as you materialize and you cannot see anything clearly for 30 seconds. Luckily, the death penalty isn't very harsh. Players suffer a temporary reduction in stats as they are transported to a "loading area." The loading area can be considered one of the worst places in the game, since the resolution is fixed at a low setting with no options to make it look better. Not only does this screen make the game look bad due to its graininess, but it's also a huge time waster. Players that die have to go through two loading screens in order to get back into the action - one screen to get to the load area, and another just to regain entry into the Matrix, completely wrecking the pacing of the game.

The draw of playing The Matrix Online comes from having an influence on how the overall story turns out. At key points, the static text will switch over to voice actors who further the story along. Some of these moments feature the voices of actors from the movies. Then there are areas in the Matrix (known in the game as Metro City) that are taken directly from the movie, furthering the Matrix-like feeling. The gameplay isn't much different from other MMO games, where you have to go on missions, beat up random thugs, gain xp, and keep leveling up to get more abilities. However, the most intriguing aspect of combat is the interlock melee mode, which will send players into one-on-one combat with enemies. Here, players select different styles to use against opponents. Every move comes down to a role of the dice to determine whether they are effective or not, so it oftentimes seems like luck plays a greater role in determining things than skill does. Interlock combat is amusing and unique, but can sometimes be frustrating. It is very difficult to run away once caught in interlock, sometimes making accidental kill stealing almost unavoidable. Additionally, when multiple players try to battle a single target on one team, there is more chaos involved in fighting than style. Not to mention, occasionally, an enemy will catch you, and the camera will fly into a bad perspective for a few seconds (like behind a sign or into a wall), obscuring the view and giving the opponent a few free hits.

Going on missions can be an uneven experience. For many of the early levels, the missions feel very similar. Teaming with other players can be difficult too, since there is very little in the way of keeping track of where your teammates are. It's easy to lose one another, especially if someone dies and has to go back to the loading area. The Matrix Online also has some interesting tools, like built in AIM to contact the outside world and the ability to stream internet music directly into the game. These tools are undermined by the clumsy and unintuitive interface. For example, there is no way to import an AIM buddy list or quickly reply to people who message you.