Mr. Fish [Nick Offerman] lives in a coral reef society that feels glum and dreary, tucked away from the sunlit world above. The arrival of a baby sea dragon named Pip [Nina Oyama] at his shipwreck home gently pulls him into a new, hopeful orbit. Pip needs help expanding her home to accommodate hundreds of siblings, a mission that would give many of her kin a place to thrive. At first, Mr. Fish resists the idea, preferring the quiet of his own gloom. Yet when both his home and Pip’s are destroyed in the chaos that follows, he reassesses his priorities. Rather than simply rebuilding, Pip proposes a quest to seek out Shimmer [Jordin Sparks], a mysterious fish said to grant wishes, even if only intermittently.
Beneath the reef lies an abyss where a pod of cuttlefish, led by Marin [Miranda Otto], faces a dire predicament: kelp growth has started to block the sun, threatening their ability to live and their future in the reef. The pressure to relocate weighs heavily on Marin’s group, while her son Benji [Remy Hii] resists leaving his home and chooses to chase the possibility of Shimmer himself. The chase becomes a contest, since Shimmer is rumored to be able to fulfill only one wish every few years, heightening the stakes for both sides.
Mr. Fish and Pip set out on their journey, moving through peril and promise as they push toward the abyss. Along the way they rescue two jellyfish, help three dolphins, and assist a mother whale in reuniting with her child, aided by a helpful eel. Their selfless acts earn them friends among sea creatures they meet, people whose loyalty will matter when the final test arrives. The pair eventually reach Shimmer, only to be interrupted when Benji storms in and abducts her, dragging her back toward the abyss with others in pursuit.
The arrival of Shimmer at the abyss signals a dramatic turn: she reveals that she cannot actually grant wishes. The revelation triggers a dramatic upheaval, as the cuttlefish relocate to the reef above and Marin publically disowns Benji, distancing the family from his reckless quest. The cuttlefish begin to hypnotize residents into exile, a dark turn that threatens the entire ecosystem. In response, Mr. Fish and Pip rally the animals they helped along the way, calling in every ally they earned to stand with them against the looming crisis. Together they manage to strip away the kelp that blocks sunlight, restoring safe passage and allowing the cuttlefish to return to their homes.
With the reef restored, Mr. Fish’s own home is rebuilt, and Pip’s family finally finds a fitting new residence aboard a cruise shipwreck designed to accommodate all of her siblings. Pip also reveals to Mr. Fish that she wrote a story titled The Pout-Pout Fish, a tale that the film is depicting within its world. As Pip departs, Mr. Fish is left to confront what’s next, only to be surprised by a reunion with Shimmer, whom he attempts to ask out—an invitation that remains tangled in the echoes of the day’s chaos, as the eel’s misstep may have triggered the very events that reshaped his life once again.
