Ninja Nonsense is an absurdist comedy, and as such there is no multi-episode story arc and very little plot within individual episodes. The characters essentially ‘reset’ at the beginning of each show, much like other absurdist comedies such as Galaxy Angel or Mini-Goddesses.
In the first episode Shinobu, a ninja apprentice, is attempting to pass her ninja exams while Kaede, a normal schoolgirl, studies for her school exams. As a part of her exam, Shinobu is ordered to break into Kaede’s room to steal her panties by her instructor, Onsokumaru. Shinobu, who despite her enthusiasm, possesses little if any actual ninja skills, believes herself to be invisible and ’sneaks’ into Kaede’s room. Since Shinobu is perfectly visible to Kaede, the mission doesn’t go as planned. Despite all of this, Kaede takes pity on Shinobu and the two become close friends.