During the years 1985 to 1988, near the Cape of Storms, a unique animal military unit known as H.M.M.F. (Hydro Marine Military Force), comprising two cape fur seals—the seasoned Claggart, portrayed by J.K. Simmons, and the tech-savvy Switch, along with a celebrity striped dolphin named Dolph, played by Dolph Lundgren, embarks on a critical mission to neutralize a naval mine. However, due to Claggart's color-blindness, he mistakenly cuts the wrong wire, leading to a catastrophic blast when the mine is brought aboard their vessel, the Good Boy. This explosion devastates part of the ship, causing it to wreck on a rock while the H.M.M.F. members survive unscathed. Unfortunately, Claggart loses his name tags, which drift to Seal Island, an area teeming with seals.
As time passes, the retired members of H.M.M.F. find their paths diverging: Claggart remains at the wreck of the Good Boy, while Switch becomes unhinged, creating a lab from his wreck, inhabited only by his imaginary companion, Senior Echo. Meanwhile, Dolph rises to fame in the entertainment industry with a superhero show titled Dial Eck-Eck-Eck-Eck For Action.
Fast forward to the present day, Claggart’s name tag is discovered by an adventurous cape fur seal named Quinn and his anxious friend Benji as they search for food. This occurs amid threats from sharks, a constant fear for their community, often dismissed by their elder leader, Brick. Faced with a food shortage, the seals are reduced to consuming unappetizing barnacles while awaiting the annual sardine run. After finding the name tag, Quinn and Benji's nighttime hunting expedition leads them into a confrontation with a great white shark named Grimes, with tragic consequences for Benji, who becomes the shark's prey.
Quinn narrowly escapes by hiding in the wreck, just as an elderly Claggart arrives to fend off Grimes, reclaiming his name tag before leaving. When Quinn regains consciousness, he encounters three cape gannets—Diving Dee, Roger, and Mayday—who guide him to the Good Boy. Driven by a longing for revenge, Quinn persuades Claggart to teach him how to combat sharks after witnessing his earlier encounter with Grimes.
Following Claggart's advice to form a team, Quinn returns to Seal Island and recruits the quirky but enthusiastic Beth, as well as the boastful yet timid Great Geraldo, who never misses a chance to share tales of escaping an aquarium in Cape Town, where he left behind his girlfriend, Magnificent Jing. Upon reaching the Good Boy, Claggart imparts vital skills to the team, ensuring they pass their final training assessment. That same night, at Quinn's urging, Claggart takes them to Switch's wreck, where they gain access to new gadgets including snapping clam grenades, electric eel bolts, and an ensemble of octopuses named Flicka, capable of rendering anyone invisible.
With newfound skills and gear, they confront a shark successfully. However, a pair of onlooking sharks inform Grimes, who plots to make an example out of them by summoning sharks from across the seas. Aware of the looming danger, Switch suggests employing his special chum formula to hypnotize the sharks and lure them away from Seal Island. They venture to Cape Town to procure a boat for their mission, where Geraldo reunites with Jing. He ultimately confesses that she was the mastermind behind his failed aquarium escape, prompting her decision to join their ranks.
Back at Seal Island, they deploy the chum strategy against the sharks with assistance from their weapons. An ambush leads to a crash, where a remora that gets left behind divulges Grimes’ strategy of surrounding Seal Island with a growing shark army. Geraldo and Jing devise a distraction, using replicas to lure the sharks away while the others regroup to uncover Grimes’ true plot.
With Flicka’s help, Quinn infiltrates Grimes' lair within a sunken oil tanker, leading a counterattack against the sharks. Their efforts turn the tides as the seals shed their fear and join the fight, which ultimately includes Brick and an unexpectedly alive Claggart, who enlisted Dolph for their cause. Together, they revive the Good Boy, providing a means for the seals to escape. In a climactic showdown, Grimes confronts Quinn in a tug-of-war over Claggart's name tag, but Quinn prevails, causing Grimes to meet his end by the ship's propeller.
Six months later, Quinn and his comrades establish the Good Boy as their new base on Seal Island, celebrated as heroes by its inhabitants. They, along with the gannets and Dave—their amusing shark ally—remain ever vigilant against any seal threats.
In a series of humorous mid-credits scenes, Dave appears as a guest on a talk show, showcasing his amusing misadventures involving various objects he mistook for plankton, shedding light on the notion that not all sharks harbor ill intentions.
