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.
Although this is a ninja-themed series, most of the twenty-four stories are self-contained snippets of Shinobu's life and dealings with her zany instructor, Onsokumaru and other ninja (sometimes referred to as the Sasuke Army). They are often accompanied by Kaede acting as the only voice of reason among the otherwise madcap characters. The series concludes with the Sasuke Army breaking the fourth wall and discussing how the anime should actually end, briefly exploring each of the options before ending on a positive note reinforcing the friendship between Shinobu and Kaede.
