The Xbox and PlayStation 2 versions have a Spy vs. Upsilon mode, with players able to play as Echelon Spies or the Upsilon agents, and also has a co-op mode intertwined with the single player portion of the game.
There are 6 Game Modes in these Spy vs. Spy matches: Team Hack, Deathmatch, Team Deathmatch, Key Run, Sam Vs. All, and Countdown. Team Hack has players trying to retrieve data by hacking into enemies' computers and securing their own computers, similar to "Capture the Flag". Deathmatch and Team Deathmatches pit players against each other. Key Run is similar to Team Hack, except retrieving a Key to hack into the other team's computer is the main item to capture. Sam Vs. All is reminiscent to Metal Gear Solid 3: Subsistence's Sneaking Mission game mode, in which one player who is Sam Fisher must play as a lone wolf and hack into computers defended by an Upsilon spy team. However, the key difference is that Fisher lacks the equipment from the single-player mode, and is nearly identical to normal spies. Countdown is similar to Deathmatch, except players must outlast each other by getting more kills to extend their time limit.