For the first time in the history of the Metal Gear franchise, the game now provides an online gameplay environment. In the new Online Mode, gamers can choose their mission and rules, including Team Battle and Snake and Enemy (one person becomes Snake and the other person blocks out his mission), and then fight it out online. This new mode also brings the classic Metal Gear Solid combat elements into online play, such as the Close Quarters Combat (CQC) proximity encounters, stealth and sniping.

Metal Gear Solid 3: Subsistence has also added the option of the Third Person View Camera for every stage of the game. This wider field of vision and complete freedom of movement brings an incredible sense of realism to the game. Gamers will have an easier time spotting enemies on-screen and preparing for their next stealth maneuver.

Metal Gear Solid 3: Subsistence also contains the original versions of Metal Gear and Metal Gear 2: Solid Snake that were previously released only in Japan for the MSX2 game console. These titles, based on the concept of infiltrating the enemy base using stealth tactics, rather than eliminating all of your enemies, were an innovative take on the action genre, proposing an entirely new approach to gameplay. Metal Gear Solid 3 is set in the 1960s, before the events of the MSX2 titles. Bringing Metal Gear and Metal Gear 2: Solid Snake to the PlayStation®2 computer entertainment system gives gamers more information about the storyline in what happens following the events of Metal Gear Solid 3.