Deep in Tokyo Bay, two hundred meters below the surface, lies the Magmell Deep Sea Aquarium, the only aquarium in the world built within the deep sea itself. The name Magmell carries the meaning of land of the dead, reflecting how the deep sea is a place where death rains down and dead matter is consumed to fuel the next cycle of life. The aquarium was built to be a small light in that darkness, a place where people can come face to face with the mysterious creatures that inhabit the abyss.

The story centers on Kotaro Tenjo, a young man who has been fascinated by deep-sea life since childhood, thanks to his father, a renowned deep-sea photographer named Koyo Seno who vanished without a trace six years earlier. Kotaro lands a part-time job as a cleaner at Magmell, but his true dream is to become a full keeper. He is shy and quick to apologize, yet when the topic turns to deep-sea creatures, he becomes unexpectedly eloquent and passionate. His encounter with the aquarium's director, Minato Osezaki, changes everything. Osezaki, a deep-sea specialist with a gruff exterior and a deep understanding of the creatures in his care, recognizes Kotaro's sincere love for the animals and promotes him to a cleaner and assistant keeper position.

The narrative unfolds through a series of episodes centered on different deep-sea species, each chapter weaving scientific facts about the creature into the emotional journeys of the people connected to the aquarium. Kotaro struggles to earn the trust of Micchan, a female Mitsukurina anglerfish that is the aquarium's unofficial mascot, learning about the species' parasitic mating habits and the fragility of their skin. He helps rescue a wild Greenland shark, one of the longest-living vertebrates on Earth, that has become stranded and unable to return to the deep. He prepares a public presentation on the bioluminescent helmet jellyfish and finds a creative way to make them glow for the audience by using the same tank as Micchan, whose presence helps the jellies feel secure enough to emit light.

The cast of characters expands to include the people who make the aquarium function and those who visit it. The aquarium's staff includes Izuho Haruno, a large and perpetually low-energy veterinarian who takes a serious view of every life that comes from the sea; Asahi Yui, a cool and seemingly aloof keeper who hides a caring heart; and Shizuka Nagaizumi, a gentle female keeper who encourages Kotaro to speak with love about the animals. The aquarium also draws visitors whose personal struggles mirror the adaptations of the deep-sea creatures. A stressed schoolteacher who faints in front of the nautilus display finds encouragement from Yui, who compares her situation to how the nautilus retreated to the deep when faster ammonites outcompeted it, surviving the extinction that wiped out its rivals.

Outside the aquarium, Kotaro forms friendships with a young chef apprentice named Ran Dogashima, who works in the aquarium's submarine-themed restaurant Latimeria and dreams of creating the world's best deep-sea cuisine, and a taciturn fisherman named Shinya Shirahama, who works under the elderly captain Okijiro Sagara. Together they navigate the ethical complexities of cooking the same creatures the aquarium works to protect and preserve. A recurring thread throughout the story is the disappearance of Kotaro's father, which is gradually revealed to be connected to Osezaki himself. The two men were once close friends, but after Osezaki's wife Nagisa died shortly after giving birth to their daughter Nagisa, Osezaki pushed Koyo away with harsh words, and Koyo left home shortly afterward. As Kotaro grows closer to Osezaki and learns the truth about his father, he begins to understand the weight of the past and his own path forward.

Later volumes introduce a new part-time cleaner, Ryo Chibata, a high school student who has been hiding his true self and wearing a false persona. Through his work at the aquarium, inspired by the creatures living as they are in the deep sea, he begins to find the courage to step toward his real identity. As Kotaro's training progresses and he is confirmed for a full keeper position after his internship, the story shifts to explore Osezaki's own past, his frail health as a young man, his difficult search for meaning, and the transformative journey that led him to build the Magmell Deep Sea Aquarium.