Metal Gear Solid 2: Substance is the expanded re-release of Sons of Liberty. Featuring a whole host of VR Missions, alternative missions and Snake Tales, the game set out to correct the initial backlash regarding the change in main character role for Sons of Liberty. With a whole new list dog tags implemented into Sons of Liberty, which was included as part of the Substance disc, the game added replay value to a game many had already completed many times. Exclusive to the PlayStation version was in the inclusion of a skateboarding mode. The skateboarding mode consisted of the unlockable MGS content in Konami's skating game - "Evolution Skateboarding".

Also included in the "collectors edition" of Substance was The Document of Metal Gear Solid 2. In short, The Document is an interactive making of disc which enables players to play around with character models, level maps and even Metal Gear. Also included on The Document of Metal Gear Solid 2 were things like a translated game script, character sketches, abandonned concepts and every cutscene in the game. The cutscenes could be paused at any time and the player had full control over the camera, enabling them to watch cutscenes from different angles and take a closer look at background details.