Released on June 25, 1999, for the PlayStation in Japan, Metal Gear Solid: Integral is an expanded edition of the game that features the added content from the American and European versions. It replaces the Japanese voices from the original version with the English dub, offering players a choice between Japanese and English subtitles during cutscenes and CODEC conversations (item descriptions, mission logs, and other text are still in Japanese). Further additional content to the main game include an alternate "sneaking suit" outfit for Meryl (which she wears when Snake is dressed in the tuxedo), a "Very Easy" difficulty setting where the player starts the mission armed with a suppressor-equipped MP5 submachine gun with infinite ammo (substituting the FAMAS rifle in Snake's inventory), an eighth Codec frequency featuring commentary from the development team (unvoiced and in Japanese text only) on every area and boss encounter, hidden music tracks, an alternate game mode where the player controls Snake from a first-person perspective (on Normal difficulty only), an option for alternative patrol routes for enemies, and a downloadable PocketStation minigame. The Torture Event was also made easier, reducing the number of rounds to three per session on all five difficulty settings.

The VR training mode is now stored on a separate third disc, known as the "VR Disc", and has been expanded into 300 missions. These new set of missions are divided into four main categories: Sneaking, Weapons, Advanced, and Special. The first three categories feature standard training exercises that test the player's sneaking, shooting, and combat skills, while the fourth category contains less conventional tests involving murder mysteries, giant genome soldiers, and flying saucers. One particular set of missions has the player controlling the Cyborg Ninja, unlocked by either completing a minigame on the PocketStation and uploading the data to the VR Disc or by achieving the Fox rank on the main game. Completing all 300 missions will unlock a concept artwork of Metal Gear RAY, a mech that would later appear in Metal Gear Solid 2: Sons of Liberty. Additional content includes preview trailers of Metal Gear Solid from trade events and a photoshoot mode where the player can take photographs of fully expressive polygonal models of Mei Ling and Dr. Naomi after completing the main game. Famitsu magazine rated Metal Gear Solid: Integral a 34 out of 40.

The VR Disc from Integral was released by itself during the same year in other regions as Metal Gear Solid: VR Missions in North America on September 23 and as Metal Gear Solid: Special Missions in the PAL region on October 29. While the content of both, VR Missions and Special Missions, are virtually identical to the VR Disc, the unlocking requirements for the Ninja missions and the photoshoot mode were changed accordingly, so that save data from the main game was no longer required. The Special Missions version also adds an additional requirement in which the user must also own a copy of the original Metal Gear Solid in PAL format in order to start the game - after booting Special Missions on the console, the player will be asked to switch the disc with the first disc from Metal Gear Solid to load data before asking the player to switch back to the Special Missions disc to proceed through the rest of the game.