The goal of Subnodule is to collect every manganese nodule on the screen. Each nodule is worth 500$, but you lose 50$ if you shoot one by accident. Once this is completed, your sub is transported to the next area. Sea monsters, alongside bombs and other subs, will try to hinder your progress. Each hit takes away one of your five remaining submarines; when you lose all five, the game ends.
Subnodule features a high-score mechanic, where at the end of your game you can save your total points to the disk. The high-score that comes with the game was set by the game's programmer, John Romero.