Valis II has the same basic plot as its computer counterpart: Rogles, the tyrant of the magical world Vecanti, was defeated, and a new emperor named Megas is terrorizing its inhabitants. It's up to the Japanese schoolgirl Yuko to take on her persona of the Valis Soldier and vanquish Megas.

Gameplay-wise, this version differs from the computer releases significantly. Though it has six stages that end with the same boss enemies, its level design, layout, and many regular enemies are different. This release also completely removes two key gameplay features of the computer version: the ability to equip different weapons and armor, and the flying side-scrolling shooter stages.