During a codec conversation in the Jungle Maze, Campbell will say that the radar is being jammed by a substance called "Minovsky molecules". This is a reference to "Minovsky particles" from Mobile Suit Gundam, which have several effects including radar jamming.

Many plot elements of Metal Gear 2 were later re-used by Metal Gear Solid on the PlayStation, such as Snake having a rematch with an old foe (Grey Fox), a temperature-based shape memory alloy key (Gustava's brooch/The PAL key), following a female soldier in disguise into a ladies' bathroom (Gustava/Meryl) and Grey Fox secretly giving Snake advice over the radio (#1 Fan/Deepthroat).

The character portraits were copied from famous films and icons.