

Battle A competitive 2-player mode that requires a Game Link Cable, along with an additional Game Boy Color unit and a second copy of the game cartridge. Most of the missions are recreations of the ones featured in Metal Gear Solid: Integral Vs. VR Training 180 training missions spread across three main categories (sneaking, weapon and advanced) and various sub-categories within each. In this Special training mode, the player controls an unknown agent who goes through a VR recreation of Snake's mission in Galuade, while being supervised by a mysterious entity named 'No.4.' As the player clears more of these stages, No.4 will disclose details of the game's story not revealed in the main campaign. After the Story mode is completed, 'Special' versions of the stages become available where the player must achieve new objectives (such as collecting FOXHOUND emblems or reach the goal without being seen). Stage Select Allows the player to replay previously cleared stages in order to achieve a higher ranking. In addition to the main story mode, Ghost Babel offers the following alternate game modes. Like in previous installments, the player communicates with various allies via a wireless communication device (the Codec), which is also used to save the player's progress. Crawling is now assigned to the Start button (instead of pressing two buttons simultaneously) and the changing of weapons and equipment is done on the main game screen rather than on separate sub-screens.

Depending on the difficulty, the number of punches required to defeat an enemy soldier differs and in the higher difficulty levels, the enemy soldiers will be knocked unconscious for a while after the first series of punches instead of simply being defeated. By flattening himself, Snake can move across the wall (allowing him access to tight passages that are not accessible by walking), scroll the camera behind his position to scout the area ahead, or knock the wall to lure nearby enemy soldiers. Snake now has the ability to flatten himself into walls like he does in Metal Gear Solid.

Moreover, all the characters in the game now move in eight directions, allowing both the player and the enemies to move diagonally in addition to the four cardinal directions. One difference from the MSX2 games is that the screen now scrolls when Snake moves throughout 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 in the series, the objective is to infiltrate the enemy's stronghold while avoiding detection from guards or surveillance systems. Ghost Babel follows the overhead 2D format used in the 1990 MSX2 game Metal Gear 2: Solid Snake while adding a few new elements introduced in Metal Gear Solid.
