Unlike the console installments, Ghost Babel uses a stage-based structure, with a total of 13 stages and doesn't have a multiple playthrough option.

Like in Metal Gear 2 and Metal Gear Solid, the player can use the Codec to receive information from allies and save their progress. Almost all the weapons in Metal Gear Solid are included with the exception of the Stinger missiles, which required the use of the radar in Metal Gear 2, and the sniper rifle. The player can also lean into walls and move the position of the camera above Snake's back like in Metal Gear Solid and tap walls. Another difference is that Solid Snake can now move in eight directions instead of four, allowing him to move diagonally in addition to the four basic directions.

Unlike the earlier MSX2 games, the game's screen scrolls while the player is moving through a single area instead of using flip screens. The player can acquire numerous items and weapons to help them fulfill their mission. As with previous games, the objective is to infiltrate an occupied enemy base while avoiding detection from guards and surveillance systems. The gameplay format is largely similar to the previous 2D Metal Gear game, Metal Gear 2: Solid Snake, in addition to several elements from Metal Gear Solid. Ghost Babel uses the same overhead view of the early Metal Gear games for the MSX2 and Nintendo Entertainment System.

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