The story takes place in Tokyo Butei High School, a special school where armed detectives—"Butei"—are trained to use weapons. Kinji Tooyama is a second-year-student who has a special ability, but he keeps it a secret to maintain an ordinary, peaceful life; however, when he gets caught in a bombing on the way to school, he encounters H. Aria Kanzaki, the most powerful S-Rank Butei student in Assault Studies.

A few years after they first met, Naomi Armitage and Ross Syllabus have started a family. Despite their normal lives, they must keep their identities a secret because many people believe that Robots do not deserve equal status with humans. Ross has an opportunity to abolish these ideas on Earth through a vote, but organizations in the shadows are working so that it doesn't happen.

To save the Earth from alien invaders and their giant monsters, Dr. Kishida does what any other red-blooded mad scientist would do: he builds a giant robot—the ultimate feminine fighting robot! Unfortunately, his grand-daughters refuse to pilot it! Apparently, they've got more important things to do than becoming teenage super-heroes. Besides, how are you supposed to study for your college entrance exams while getting beaten-up in battle? Fortunately for Dr. Kishida, things aren't too well for the invaders, either. According to their reports, the Earth was the perfect target: lush, peaceful, and relatively defenseless. Theoretically, the planet should've surrendered long ago. Now, the war is at a standstill, the dreaded Accounting Department is warning about the serious cost overruns, and the head of the home office has arrived from Galactic Headquarters to personally oversee operations. Has Headquarters decided to unleash, The Audit—or do they have something even more evil in mind? The fate of the world rests upon two people: Aya Kishida, one of the doctor's granddaughters, who may have to give up prep school to pilot the mighty (and lovely) ARIEL; and a mysterious alien named Saber Starblast, who may have the power to defeat the invaders once and for all...

Koro-sensei reminisces about his first meeting with Karasuma, where they first butted heads and fought against each other, ultimately coming to respect one another. However, Karasuma eventually points out their actual meeting wasn't nearly as eventful.