"Saishū Shiken Kujira" is a science fiction anime series set in a dystopian future where humanity faces extinction due to environmental collapse and the emergence of monstrous creatures known as "Kujira." These creatures, resembling massive whale-like entities, roam the skies and seas, rendering the planet uninhabitable. The story centers on a group of young individuals who are part of a government program designed to combat the Kujira threat. These youths, known as "Test Subjects," are genetically engineered and trained to pilot advanced mechs called "Vessels," which are humanity's last hope for survival.

The protagonist, Akira, is a reserved yet determined teenager who becomes a Test Subject after losing his family to the Kujira. Alongside him are other Test Subjects, each with their own motivations and struggles, including Rei, a fiercely independent and skilled pilot, and Haruto, a compassionate but conflicted individual burdened by the weight of his responsibilities. The group is overseen by a mysterious organization that conducts the "Final Whale Examination," a series of high-stakes missions aimed at understanding and ultimately defeating the Kujira.

As the series progresses, the Test Subjects uncover unsettling truths about the origins of the Kujira and the true purpose of the government program. The narrative explores themes of sacrifice, identity, and the ethical implications of genetic engineering and human experimentation. The characters grapple with their roles as weapons of war and their desire to reclaim their humanity, all while facing increasingly dangerous Kujira threats. The story builds toward a climactic confrontation that challenges the characters' resolve and forces them to confront the consequences of their actions in a world teetering on the brink of annihilation.