"Princess Army" centers on a group of young women who are recruited into a military academy designed to train elite soldiers capable of defending their nation against a looming extraterrestrial threat. The narrative unfolds in a near-future setting where humanity faces invasion from advanced alien forces. The academy, known as the Royal Military Institute, is a prestigious institution that combines rigorous combat training with advanced technological education. The protagonist, Aya Fujisaki, is a determined and resourceful cadet who joins the academy with a personal vendetta against the alien invaders after her family is tragically killed in an attack.

Aya is joined by a diverse ensemble of cadets, each with unique skills and backgrounds. Among them is Rina Tachibana, a skilled tactician with a calm and analytical demeanor, and Miki Shindo, a hot-headed but fiercely loyal fighter. The group also includes Haruka Minami, a prodigious engineer who designs cutting-edge weaponry, and Yuki Nakamura, a mysterious and reserved individual with a hidden past tied to the alien forces. Together, they form the core of the "Princess Army," a specialized unit tasked with piloting advanced mecha suits and executing high-stakes missions.

The plot progresses as the cadets undergo intense training, facing both physical and psychological challenges that test their resolve and teamwork. Early episodes focus on their struggles to adapt to the academy's demanding environment, with interpersonal conflicts and rivalries adding tension to their journey. As the alien threat escalates, the cadets are thrust into real combat scenarios, where they must rely on their training and each other to survive. Key missions include infiltrating enemy strongholds, protecting civilian populations, and uncovering the aliens' true motives.

A central subplot involves the discovery of a hidden alien artifact within the academy, which holds the key to understanding the invaders' technology and origins. This artifact becomes a focal point of the story, as both the cadets and their superiors grapple with its implications. The narrative also explores themes of sacrifice, loyalty, and the moral complexities of warfare, as the cadets are forced to make difficult decisions that challenge their ideals.

The series builds toward a climactic confrontation between the Princess Army and the alien forces, with the fate of humanity hanging in the balance. Along the way, the characters undergo significant development, with their individual arcs intertwining with the larger narrative. Aya's journey, in particular, serves as the emotional core of the story, as she confronts her past and finds new purpose in her fight for the future. The series concludes with a resolution that ties together the central plot threads while leaving room for potential future developments.