"Jellyfish Can't Swim in the Night" centers on a group of four high school girls who form an artistic collective called JELEE, aiming to create music and multimedia projects that reflect their shared struggles and aspirations. The protagonist, Mahiru Kozuki, is a former idol who quit her group due to disillusionment with the industry. She crosses paths with Kano Yamanouchi, a reclusive artist who creates jellyfish-themed illustrations under the pseudonym "JELEE." Inspired by Kano's work, Mahiru proposes a collaboration, and the two are joined by Kiui Watase, a talented but insecure composer, and Mei Takanashi, a vlogger with a sharp wit and a knack for video editing.

The narrative explores the challenges each girl faces in balancing their creative ambitions with personal insecurities and societal expectations. Mahiru grapples with the fallout of her idol career and her desire to redefine herself through music. Kano struggles with social anxiety and the pressure to live up to her online persona. Kiui confronts her fear of failure and the weight of her family's expectations, while Mei navigates the complexities of online fame and her evolving identity. Together, they channel their struggles into their art, using JELEE as a platform to express their individuality and connect with others.

The series delves into themes of self-discovery, the power of collaboration, and the intersection of art and identity. As JELEE gains recognition, the girls face external pressures and internal conflicts that test their resolve. The story balances moments of introspection with the dynamics of their growing friendship, culminating in a climactic performance that symbolizes their collective growth and resilience. Through its exploration of creativity and personal growth, "Jellyfish Can't Swim in the Night" offers a nuanced portrayal of adolescence and the transformative potential of art.