A scientist has been conducting an experiment that went wrong... very wrong. An explosion shattered the house. Afterwards, a cute little toy named Michael opened his eyes... to find out that he is, indeed, alive. He can think, talk, and walk now. The first decision he makes is to check on the three lovely daughters of the scientists: Hikari, Nozomi, and Tsubasa. To his (and their) astonishment, the failed experiment made all the three girls tiny! Now Michael and the girls have to find the crazy Dad and somehow revert everything back to normal.

Minimum Nanonic is a traditional Japanese adventure, with the story either unfolding automatically, or triggered by selecting verbs from the menu ("Look", "Think", etc.). There are no wrong choices, and it is impossible to die in the game. If Michael makes a wrong decision, he will simply refuse to do what he chose, and the player will have to try another option.