Himawari Hinata transfers to Shinobi Gakuen in the Village of Mist, driven to become a kunoichi after a childhood rescue by a ninja. On her first day, non-ninja teacher Hayato Marikoji saves her from a kite mishap. Spotting a distinctive mark on his neck matching her childhood rescuer's, she addresses him respectfully as "Hayato-dono."

Determined yet initially unprepared for ninja life, Himawari faces classmates who view her as unskilled and sometimes annoying. Undeterred, she focuses solely on becoming a capable kunoichi. She befriends peers: Azami, an information collector posing as a girl; Shikimi, a serious herbal medicine student; Yusura, who communicates with animals; and Himeji, a weapons specialist. Her relationship with Hayato deepens beyond teacher-student dynamics, fueled by her suspicion of his link to her past savior, compelling her to protect him.

Her abilities develop through the academy's rigorous training. Starting with struggles in fundamental techniques, she gradually hones her skills, facing classroom challenges and missions. Her growth highlights perseverance through setbacks rather than innate talent.

The mark on Hayato’s neck persistently fuels her belief in his hidden significance, strengthening her protective instincts and commitment to her training and his safety. Classmate relationships add dimension: Yusura’s bond with her pet Momota and kappa boyfriend Yonezawa, or Shikimi’s cautious friendship with Nanafushi, illustrating Himawari's integration into the academy.

Her arc focuses on proving herself worthy of Shinobi Gakuen while navigating the mysteries around Hayato. She confronts academic hurdles and participates in village activities, steadily progressing. The story concludes with her ongoing development as a kunoichi-in-training, leaving Hayato's potential connection purposefully unanswered.