In the year 2356, humanity faces an existential threat following the catastrophic event known as the "Great Collapse," caused by a nearby supernova. The explosion's shockwave, called the "Wave," destroyed much of Earth's infrastructure and wiped out a significant portion of the population. To prepare for the impending arrival of a second, more destructive wave, humanity constructs massive space stations, including Stellvia, a state-of-the-art facility dedicated to training young pilots and engineers to defend Earth.

The story centers on Shima Katase, a brilliant but socially awkward teenager who enrolls at Stellvia to become a pilot. Despite her exceptional mathematical and technical skills, Shima struggles with self-doubt and a fear of failure, stemming from her inability to save her younger brother during the Great Collapse. At Stellvia, she befriends a diverse group of classmates, including the confident and outgoing Kouta Otoyama, the reserved and disciplined Akira Kayama, and the enigmatic Rinna Kazamatsuri. Together, they navigate the challenges of rigorous training, interpersonal conflicts, and the looming threat of the second Wave.

As the students progress, they are divided into teams to participate in simulations and real-world missions. Shima's team, led by Kouta, demonstrates remarkable synergy, with Shima's analytical mind complementing the others' skills. The narrative explores their growth as individuals and as a team, highlighting their struggles with personal insecurities, societal expectations, and the weight of their responsibilities. The stakes escalate when the second Wave arrives earlier than predicted, forcing the students to confront their fears and work together to protect humanity.

The series also delves into the broader political and scientific efforts to combat the Wave. Key figures, such as Professor Yamato and the mysterious pilot known as "White Symphony," play pivotal roles in developing strategies and technologies to mitigate the disaster. The narrative balances the personal journeys of the students with the larger-scale efforts of humanity, creating a cohesive story that intertwines individual growth with collective survival.

"Stellvia of the Universe" combines elements of science fiction, coming-of-age drama, and space opera, presenting a narrative that emphasizes teamwork, resilience, and the human capacity to overcome adversity. The characters' development is central to the story, with their relationships and personal struggles driving much of the emotional weight. The series concludes with a climactic battle against the second Wave, showcasing the culmination of the students' training and their unwavering determination to safeguard the future.