The flightless birds and scheming green pigs take their feud to the next level.
Red has been trying to keep up his reputation as a hero to the birds on Bird Island by protecting them from the pigs on Piggie Island. However, King Leonard calls for a truce when they are threatened by Eagle Island and its leader, Zeta, who is using ice balls to wreck both islands and get rid of the inhabitants to make the islands her own paradise. Red forms an uneasy alliance with Leonard and teams up with Chuck, Bomb, Leonard’s assistant Courtney, and Chuck’s sister Silver to save their islands.
The team sneaks onto Eagle Island with Mighty Eagle, but he retreats after revealing that Zeta was his ex-fiancee that he stood up when he got scared. The birds and pigs try to disable Zeta’s weapon that is launching the ice balls, which she is now filling with lava. After infiltrating the lab with the weapon, the birds and pigs manage to destroy it. Zeta and Mighty Eagle reconcile, and they are later married and become parents to Debbie, the daughter that Mighty Eagle never knew he had.
Red is once again credited as a hero for saving the islands, but he shares the credit with his friends. Red and Silver then start a relationship, even though Chuck is not too fond of it.
A subplot involves Terence and Matilda’s daughter Zoe and her two friends Vivi and Sam-Sam having to get back Zoe’s unhatched sisters from a bunch of trouble.
The birds and pigs are in constant war against each other after Piggy Island, which was destroyed in a prior battle with the birds, is rebuilt. Eventually, an ice ball from a nearby isle called Eagle Island hits the sea near Piggy Island, forcing pigs to have a truce with the birds. Zeta, the leader of the island, is fed up with her frozen surroundings and wants to occupy the two islands by shooting ice balls to force their inhabitants to evacuate.
Meanwhile, three hatchlings, one of whom is Terence and Matilda’s daughter named Zoe, plan to act in a play using the three eggs at a beach, but the eggs drift out to sea by accident. They set sail to retrieve them, but once they catch up to them, a whale blows them into a cloud. They manage to get them down after inflating Zoe into the air but then misplace them again.
Chuck and Bomb ask Red to join in a speed dating activity, where he meets Chuck’s sister Silver and an excellent engineering student, but she deems him incompatible. Red quits the meeting and finds Leonard, the king of Piggy Island, comes to his house to negotiate. Red reluctantly agrees to build an alliance with the pigs and they recruit Chuck, Bomb, Silver and Mighty Eagle. They hold a special meeting in Mighty Eagle’s cave. When Red shows a photo of Zeta, Mighty Eagle behaves abnormally. The meeting is disrupted when an ice ball hits Eagle Mountain and destroys it, but they escape just in time.
As the team travel to Eagle Island by submarine, Red assures the civilians they don’t need to evacuate. Once there, Mighty Eagle confesses that Zeta is his ex-fiancée that he abandoned due to his cowardice, retreating to Bird Island. Red insists on fighting alone and Silver decides to follow him. They intrude the base from the mouth of the weapon only to be captured by the guards. The other team members disguise themselves as a Trojan Eagle, grab a key card in a washroom, and get into the base. The eagle guards are driven into a breakdance battle by the disguise’s unusual movement, and the team find Red and Silver have been caught. They are forced to escape when their disguise rips apart, but the guards are too busy dancing to notice.
The three hatchlings finally find the eggs on a small island, held by a python. They somehow defeat her and plan to drift back to Bird Island, but they arrive at Piggy Island by mistake. They’re greeted by three piglets and the birds travel by hot air balloon with the pigs.
As Red and Silver are confined in ice, Zeta tells them her plan to fire lava balls at Bird Island and Piggy Island, as Red regrets telling the islanders to not evacuate. After she leaves to start the countdown, Red admits to Silver that he put himself before anyone else as he’s afraid of not being liked if he’s no longer a hero. Silver frees them both using her hair, reuniting with the team. Red gives up leadership to Silver, who establishes a plan to destroy the weapon.
Silver and Red put themselves in an ice ball and roll on a rail towards Zeta’s superweapon, but the plan comes apart and it misses the target, and the whole team are confronted by Zeta and her guards. At this time, Mighty Eagle arrives to apologize to Zeta, but she quarrels with him, revealing his name as Ethan and that she raised a daughter he was unaware of named Debbie. While Zeta is distracted, Silver tells Chuck to tie up the weapon using a powerful rope she invented, which catches and decelerates the lava balls when Zeta fires them. As the rope breaks, the hatchlings and the piglets traveling above Eagle Island help grasp it. The lava balls slide back into the weapon, destroying the whole base.
Everyone escapes, and Mighty Eagle protects Debbie from being crushed by a metal plate. Zeta shows gratitude to him and they finally hold a wedding ceremony on Bird Island, with Red as the chief witness. Everyone cheers Red for saving the islands, but he reveals Silver and the team deserves the real credit instead of him, unveiling a Mount Rushmore-style monument to them. To his surprise, Red finds he is beloved even more now because of his honesty and selflessness. The birds have a huge party to celebrate while Red and Silver begin a romantic relationship, until Chuck arrives and interrupts the two.
In a pre-credit scene, the hatchlings put the eggs back home but three snakelets hatch. The injured mother python comes and exchanges the babies with them, only for the three new hatchlings to drift out to sea again, saying goodbye to their sister.
The film starts on Bird Island, where all the little birds are enjoying a sunny day out. Red (Jason Sudeikis) has been enjoying his reputation as a hero ever since he saved everyone from the pigs. In order to maintain his status, he keeps an eye out on Piggie Island with Chuck (Josh Gad) and Bomb (Danny McBride). The pigs fire a pie at the birds on the beach. Red spots Leonard (Bill Hader) and his new assistant Courtney (Awkwafina) as they all engage in a war of throwing hot sauce, using a giant magnifying glass to burn things, and dumping a ton of crabs onto the beach. Suddenly, Leonard spots a gigantic ice ball flying in from another island. It hits the waters of Piggie Island, causing a huge splash. Leonard realizes they are in trouble.
Leonard sends a message to Red, calling for a truce. Red doesn’t buy it, but the pigs are insistent on it. Chuck and Bomb try to take Red away from his heroic duties to spend the night with them. They take him speed dating, where Red meets Chuck’s sister Silver (Rachel Bloom). She tries to determine their compatibility with her own little test, but Red doesn’t want any part in the whole scene. Silver determines that Red is afraid to talk about his feelings, so he just walks away from it.
Outside Terence (Nolan North) and Matilda’s (Maya Rudolph) house, their hatchling Zoe (Brooklynn Prince), and her friends Vivi (Genesis Tennon) and Sam-Sam (Alma Varsano) go outside to play and act out the events of Red fighting the pigs. They use Zoe’s unhatched sister eggs as part of the show, but they end up getting swept away on a raft into the ocean.
Leonard and Courtney gather information on where the ice ball came from after using a drone to gather surveillance photos. They learn that they came from the previously unknown Eagle Island. There, we meet the eagles’ leader, Zeta (Leslie Jones), who is fed up with all the ice on the island since it prevents her from enjoying anything. She works with her assistant Debbie (Tiffany Haddish) and is planning a change of scenery with both Bird and Piggie Island.
Red sulks at home by himself when he is visited by Leonard and a team of pigs. He tells Red about the ice ball, which Red had also seen near Bird Island, but he ignored it. After stressing the urgency of the situation, Red realizes that this could threaten his hero status, so he and Leonard gather Chuck and Bomb. They try to recruit Mighty Eagle (Peter Dinklage), but he appears terrified upon seeing the name Eagle Island. The guys then team up with Courtney and Silver to form their team.alls.
The hatchlings row their own raft into the water to try and rescue the eggs. When they manage to reach them, Vivi comments on how it was too easy that they got the eggs so fast…and that’s when a whale shoots water through its spout, causing the eggs to fly up and fall on a cloud.
The team gathers for their plan, but Mighty Eagle looks super nervous when he sees that Zeta is the leader, though he denies ever knowing her. The plan is to sneak into Eagle Island and disable their super weapon that is launching the ice balls. Not long after, Zeta launches another ice ball that crashes through Mighty Eagle’s cave, forcing the team to run for their lives. Mighty Eagle tries to fly them down, but crashes into a rock column. They all try to float down using their map as a parachute, but it starts to rip, so Silver thinks quickly and strings the hole up to get them to land safely. Zeta watches the scene from her surveillance cameras, but she is annoyed that the birds haven’t begun fleeing from the island. She orders her head engineer Glenn (Eugenio Derbez) to create ice balls filled with molten lava to amp up the threat.
The team prepares to leave, with Red assuring everyone that they don’t need to evacuate. Leonard pulls up a humongous submarine for them to board. Inside, they meet the pigs’ gadget developer, Gary (Sterling K. Brown). He shows off his array of gadgets, which are mostly useless.
Zoe cries over her sisters being stuck up on a cloud, so Vivi and Sam-Sam inflate her and use her as a balloon to try and reach the eggs, but they float too high and can’t undo the rope on Zoe’s beak. They float high into space until a satellite pulls the rope off and sends the hatchlings falling back down. They manage to get the eggs off the cloud, BUT they then all land on top of a sleeping boa constrictor.
Once the team arrives on Eagle Island, Mighty Eagle confesses to everyone that Zeta was his ex-fiancee, and he bailed on her at the wedding, so he is now too scared to face her. He flies back to Bird Island. Red then finds that the others came up with their own idea of using an eagle costume to try and find a way inside the lab to get to the weapon. Red tries going it alone but Silver joins him, even as he tries to get rid of her. Chuck, Bomb, Leonard, Courtney, and Gary then operate the eagle costume and fool two guards to get inside.
Red and Silver climb high enough to reach the location of the super weapon’s power source. They use a harness to get themselves down. Red gets to the floor and cuts what he thinks is the cord to the weapon, but it’s really for the microwave. He and Silver are then caught and taken prisoner. The others in the eagle costume then swipe an ID card off another guard to get inside.
The hatchlings beat up the boa constrictor and use her shed skin as boots and hats. They use a leaf as a raft to sail back to their island, only to be greeted by three piglets on Piggie Island.
The team gets inside the weapon’s room, but Chuck spots Red and Silver in captivity. They are nearly spotted as he rips their costume off, but the eagle guards are stuck having a dance party. Zeta then traps Red and Silver in ice and tells them that she plans to use the other two islands as her own little getaway resort. Silver also notes that Zeta is still clearly mad about what went on with Mighty Eagle. However, Zeta tells Red that it’s his fault that the birds are going to get hurt since he told them not to evacuate. She launches a few lava balls across the islands to show she means business. The hatchlings and piglets see their islands being attacked from a blimp they made. Red blames himself for what happens to the birds, as he was just doing this to be the hero, which leads Silver to realize that Red really cares that the other birds like him. She frees them both moments later.
Zeta prepares a countdown to start launching a whole mess of lava-ice balls on the islands. Red and Silver make their way into an ice ball to get close enough to stop the machine, while the pigs go off to try and shut the switch off, and Chuck and Bomb try to sneak past guards. Leonard and Courtney try to pull the switch, but it breaks off. Chuck rushes to get one of Gary’s gadgets to help them with the switch. Red and Silver crash their ice ball down and fail to wreck the weapon. Zeta prepares to stomp on the button to launch the balls, but Mighty Eagle swoops down after having a change of heart. He tries apologizing to Zeta, but she is still mad at him. She reveals that Debbie is their daughter and that Mighty Eagle’s first name is Ethan. While Zeta is distracted, Silver gives Chuck her string so he can move fast enough to tie around the machine. When Zeta launches the ice balls, they are pulled back and held from launching. The string starts to break, so the hatchlings and piglets keep it together long enough for the ice balls to come back down and destroy the weapon. After the dust clears, Zeta thinks she sees that Debbie is dead. She shows great remorse for her plan, but then sees that Mighty Eagle protected Debbie with his body. He then pathetically asks Zeta to take him back.
Mighty Eagle and Zeta are then married on Bird Island. Matilda then gives a speech and credits Red for his heroism. However, Red decides to give the majority of the credit to Silver, as well as the rest of his friends (except Leonard). A large Mount Rushmore-like monument is built with their faces. Everyone says they love Red even more now for being so selfless.
The birds and pigs then have a celebration for their victory and newfound truce. Red and Silver decide to have a date together, but Chuck comes to interrupt.
The hatchlings are playing together again when they decide to go see Zoe’s sisters hatch. To their shock, the things that hatch out are snakes. The boa from earlier comes with the newly hatched birds, and she gets her babies back. Zoe, Vivi, and Sam-Sam are happy to see the little hatchlings and vow to never let them out of their sights…until they do so for one moment, and Zoe’s sisters start sailing away from them, causing the three girls to faint.