Hayate Shinobu is not your regular 3rd grader; he is a fugitive ninja who keeps transferring schools in order to escape from those pursuing him.
If he gets caught, the only thing waiting for him is death.
On the other side, for the pursuers, the only way to compensate for failure in their mission is also death.
Hayate's homeroom teacher is also a ninja, and he has decided to execute Hayate to protect the ninja code, despite the objections of the Board of Education and his own anguish at the though.
Hayate must overcome numerous hardships in his pursuit of being a regular elementary school student.