Hisone to Maso-tan follows Hisone Amakasu, a straightforward young woman who enlists in the Japan Air Self-Defense Force and is stationed at Gifu Airbase, hoping military life will help her keep some distance from other people after her blunt honesty hurts them unintentionally. During a visit to a part of the base she did not know existed, she stumbles upon the JASDF's largest secret: an Organic Transformed Flyer, or OTF, a dragon with the ability to camouflage itself as an aircraft. After being swallowed up and spit out by the creature, Hisone's commanding officers inform her that she has been chosen to become the next in a long line of Dragon Pilots.
Paired with "Maso-tan," her own OTF, Hisone trains alongside fellow pilot cadets Nao Kaizaki, El Hoshino, and Liliko Kinutsugai while trying to overcome her insecurities and discover her true potential. Beneath the comedy and the unusual bond between pilot and dragon, the series builds a larger mystery around why the OTFs are hidden within the modern Self-Defense Forces and what role they may play in the future. Between military routine, awkward relationships, and sudden flights into the sky, Hisone must learn how to trust others, face herself honestly, and unravel the secrets behind the OTFs.