On Bird Island, Red has become a hero after saving the island, leading the birds in a prank war against the pigs of Piggy Island, led by Leonard. One day, a giant ice ball from the distant Eagle Island crashes near Piggy Island, prompting Leonard to call for a truce and propose an alliance with the birds. The new threat comes from Zeta, the leader of Eagle Island, who is tired of living on the island and plans to take over both islands by launching lava-filled balls of ice from her superweapon. Meanwhile, Red struggles with insecurity, fearing he will no longer be admired if peace is achieved. His friends Chuck and Bomb invite him to a speed dating event, where Red meets Chuck’s sister, Silver, an engineering student who deems him incompatible. At the same time, three hatchlings—Zoe, Vincent, and Samantha—accidentally lose Zoe’s unhatched sisters and embark on a quest to retrieve them.

Leonard visits Red and convinces him to form a team and infiltrate Eagle Island. They recruit Chuck, Bomb, Silver, Leonard’s assistant Courtney, and Mighty Eagle. The group plans their mission in Mighty Eagle’s cave but is interrupted when Zeta’s weapon destroys part of Eagle Mountain, frightening the other birds. To reach Eagle Island, the team uses a submarine built by pig inventor Garry. Red insists that evacuation is unnecessary, hoping to preserve his heroic image.

Upon arrival, Mighty Eagle reveals that Zeta was once his fiancée, but he abandoned her out of cowardice. Upon arriving, Red decides to infiltrate the weapon alone, though Silver follows him. The pair sneak into the cannon’s entrance but are quickly captured. Zeta reveals her plan to bombard the islands with lava-filled ice balls to force evacuation. Regretting his decisions, Red admits to Silver that his actions were driven by his fear of losing popularity. Silver comforts him, and together they escape.

Elsewhere, the rest of the team disguises themselves as an eagle to infiltrate the base and obtain a keycard. They reunite with Red and Silver, who devise a plan to destroy the cannon as it begins to charge. Red and Silver encase themselves in an ice ball and attempt to destroy the weapon from within, but their plan fails. As Zeta prepares to fire the cannon, Mighty Eagle confronts her and apologizes for abandoning her. Zeta dismisses him, revealing that her assistant, Debbie, is actually their daughter. While Zeta is distracted, Chuck ties the weapon using Silver’s latest invention, a type of string with enhanced durability, which slows the launched lava balls. When the string begins to break, the hatchlings, who have recovered their eggs, arrive and help hold the line. The lava balls are pulled back into the cannon, causing it to explode and destroy the base. Everyone escapes, and Mighty Eagle saves Debbie from falling debris, redeeming himself in Zeta’s eyes.

Afterwards, Mighty Eagle and Zeta marry on Bird Island as the truce continues. Red credits the team—especially Silver—for saving the islands, earning more admiration from islanders. Red and Silver begin a relationship to Chuck’s mild annoyance. Meanwhile, the hatchlings discover they mistakenly rescued a boa constrictor’s eggs instead of Zoe’s sisters. The hatchlings and the snake exchange their babies before Zoe’s sisters drift away out to sea… again..