Prologue: The Boy Samurai and The Headless Ancestor The film opens with a legend of a war between three clans. Two of them worshipped dogs while the Kobayashi clan were cat lovers. The clans fought in battle until a child warrior came forth and decapitated the head of the Kobayashi clan. Centuries later, the Kobayashi family has not forgiven their greatest defeat.
We jump ahead to twenty years in the future from now in the Japanese city of Megasaki. An outbreak of "snout fever" has been infecting dogs across the country. Mayor Kobayashi (Kunichi Nomura) issues a decree that will send all dogs to a quarantined piece of land they call Trash Island. The first dog sent there is Spots (Liev Schrieber), the pet/bodyguard of Kobayashi's orphaned nephew Atari (Koyu Rankin). The head of the Science Party, Professor Watanabe (Akira Ito), believes the dogs can be cured. Interpreter Nelson (Frances McDormand)(who translates and commentates on major events in the city) muses "Whatever happened to man's best friend?"
Part One: The Little Pilot On Trash Island, there is a pack of five dogs - Rex (Edward Norton), King (Bob Balaban), Duke (Jeff Goldblum), Boss (Bill Murray), and their leader, Chief (Bryan Cranston). The city imports bags of garbage as a means of food for the dogs. One bag drops, and Chief's pack comes across a rival pack of dogs. They get into a wild fight for the garbage, with Chief even biting off another dog's ear. His pack comes out victorious, but Rex, who is a former house pet, says he can't stomach anymore of the garbage. King, Boss, and Duke agree, as they were also domesticated, but Chief, a stray, is more thankful for what they have. The dogs then spot a female dog, Nutmeg (Scarlett Johansson), walking by.
A plane flown by Atari comes crashing down to the island. The dogs go after him when they see the wreckage. Atari has a piece of the plane stuck in his head. He sees the dogs and uses a picture to tell them he is looking for Spots. The dogs don't know him personally, but they know he's the first dog who was sent there. They bring Atari to what they believe is his cage, where a dog skeleton lies because none of the other dogs knew how to open it. Atari becomes distraught and enraged.
We see a flashback to when Atari first got Spots after the car accident that killed his parents. Kobayashi's Major-Domo (Akira Takayama) brings Spots in and doesn't appear to approve of Atari treating Spots like a pet. Atari begins to whisper to Spots, and, with tears in his eyes, he tells the boy he can understand him.
Atari attempts to leave the island. Rex notices Boss wearing the collar of the dog in the cage, and sees that the tag says "Sport" and not Spots. After Atari crashes the plane again, the dogs decide to help him look for Spots, but Chief doesn't trust Atari and refuses to help him, but the dogs overrule his decision.
At night, Chief meets Nutmeg formally. He pries into her life by asking about who she's mating with, which she doesn't approve of. After apologizing, he gets to talk to her more. Nutmeg says she is a former show dog who could perform tricks. She asks Chief if he is going to help Atari since boys like him love dogs. Chief is unsure, but ultimately agrees to go along with the mission.
At a lab in the city, Watanabe successfully discovers the cure for the canine flu. He and his assistant scientist, Yoko Ono (Yoko Ono), present their discovery to Kobayashi, but he dismisses it and plans to keep the dogs on Trash Island. He leaves the room, at which point Watanabe sees a file containing classified information regarding the canine flu and Trash Island, but the Major-Domo swipes it away from Watanabe before he can find out anything.
Part Two: The Search For Spots On their way to find Spots, the dogs start talking about their favorite foods. When they ask Chief, he reveals to them that he wasn't always a stray. He was owned by a family until he bit the hand of the oldest boy when he tried to pet Chief. He claims it was so bad that he almost bit the boy's hand off completely. The family locked him in a shed, but the grandmother brought him a bowl of hibachi chili, which he says was his favorite food. He dug his way out and became a stray.
A rescue team searching for Atari comes down along with a drone and a robot dog. The captors trap Atari, but the pack intervenes to fight them off and save Atari. Chief battles the robot dog and gets injured, but Atari is set free and he disables the robot dog. The drone also ends up crashing down to the ground.
At a school in Megasaki City, exchange student Tracy Walker (Greta Gerwig) presents a theory to her class that involves a conspiracy within the Kobayashi party, and she plans to do whatever it takes to prove that the mayor is corrupt. She organizes a televised rally with the other children to call for a reform in the way they are handling the dog situation. The kids hold up pictures of their dogs, and we learn that Tracy is Nutmeg's owner.
Atari and the dogs set out to find the dogs Jupiter (F. Murray Abraham) and Oracle (Tilda Swinton), as they are known as the wisest dogs on the island. Oracle supposedly has "visions", but she is actually just able to understand the TV and translate what's happening. Upon finding them, Jupiter and Oracle recognize Spots in his picture as "Dog Zero". Jupiter suggests that Spots may be on the island as a prisoner of a group of cannibal aboriginal dogs.
The group attempts to head further to find Spots, but Chief and Atari get split up from the other four dogs. After they land, Atari attempts to play with Chief, who is reluctant at first, but eventually warms up to the boy. He even lets Atari pet him. He then gives Chief a bath, completely removing the filth off of him to reveal that he is the same breed as Spots.
Back in Megasaki, a chef is preparing sushi. He dabs one of the rolls with poisoned wasabi and has it sent to the room of Professor Watanabe. He is reported dead in the morning from what is believed to have been a suicide. Tracy continues her investigation into the matter, even going to confront a devastated Yoko to confirm that the cure exists. Yoko gives it to Tracy so she can set out to expose the truth.
Part Three: The Rendez-Vous Atari and Chief reunite with Rex, Boss, King, and Duke as they reach a bridge that will lead them to the aboriginal tribe. The four dogs get stuck on the trash lift that they came in on, but Atari and Chief make it across. They are confronted once again by Kobayashi's men, plus more robot dogs. Just when it looks like time is up for the two, they are found by none other than SPOTS.
Another flashback shows Spots being found by the group of aboriginal dogs, but he learns from their leader, Gondo (Harvey Keitel), that they only ate their former leader because he was already sick and dying, and so the other dogs had no choice but to eat him since there was little else for them to survive off of. Gondo admits that this really hurt him and the others, but he doesn't like that they have a reputation as cannibal dogs. They find a key for Spots's cage, and they free him. Spots then meets his future mate, Peppermint (Kara Hayward).
Back in the present, Spots uses his military-issued explosive teeth to take out the robot dogs. Spots takes Chief and Atari and jumps into the river to escape the others. While they float away, Spots tells Atari that he can no longer serve him and be his bodyguard because of his new role in the tribe, and because he and Peppermint are going to be parents. He also confirms to Chief that they are brothers. Chief is at first disgusted with Spots since Atari went through all this just for him, but Spots then decides that he may now pass his former role onto Chief. Atari places Spots's mic and earpiece onto Chief, who accepts his new role.
Part Four: Atari's Lantern Atari, Chief, and Spots encounter a messenger owl sent to them from Jupiter. They learn that Kobayashi is planning to take care of the city's dog problem by effectively poisoning them with gas. Atari leads his dogs to head out on rafts back toward the city to stop this.
The city is gathered for Kobayashi's election ceremony. Atari is believed to have been dead after the bridge jump. Tracy and her classmates arrive to protest, with Tracy trying to expose Kobayashi's corruption, as well as the fact that he and his team manufactured the canine flu out of their hatred for dogs, and the fact that Watanabe was murdered. As a result, she has her student visa nullified and is set to be deported. Atari, Chief, and the other dogs arrive. They administer the cure to Chief, who is immediately relieved of the canine flu. Atari then stands up to speak and deliver a speech and a haiku, which moves Kobayashi to tears and causes him to have a change of heart. He undoes the Trash Island Decree and admits to his corruption and acting dishonorably. He tries to cancel the poisoning, but the Major-Domo tries to see the extermination through. They press a button and activate the poison, but thanks to one of Tracy's hacker friends, the poison backfires and affects the robot dogs and exterminators on the island. A robot dog then tries to attack Atari and the other dogs, but Spots intervenes and fights the robot dog. It is destroyed, but Spots loses an eye, and Atari has a metal part lodged in his head.
Atari undergoes a successful brain surgery, but his remaining kidney has failed. Kobayashi decides to donate his kidney to save his nephew's life.
Kobayashi and his whole party are locked up for their crimes. Due to the election law, Atari becomes the new mayor of Megasaki. He makes it so that all dogs are returned to their owners and that they may return to society. This helps former dog-based businesses return, including a dog treat factory that the other dogs loved. Atari and Tracy become a couple, which allows Chief to get closer to Nutmeg.
The last we see is Spots (now sporting a mechanical eye) with Peppermint and their puppies, living in the Kobayashi manor in peace.
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In the future, the Japanese city of Megasaki falls under an outbreak of canine flu. Mayor Kobayashi issues a decree to quarantine all dogs on Trash Island. His nephew, Atari, flies to the island to find his dog, Spots. Atari encounters a pack of dogs led by Chief, a stray dog who doesn't trust Atari and initially chooses not to help him, but he relents and does so.
Chief grows closer to Atari and starts to feel like a real pet to him. They eventually find Spots, who is now part of a tribe of aboriginal dogs on the island, but Spots chooses to pass on his role as pet/bodyguard to Chief, as Spots is set to become a father.
Professor Watanabe finds a cure for the canine flu, but he is murdered by Kobayashi's party to keep the dogs on the island. Kobayashi then plans to get rid of all dogs by releasing a poisonous gas. Atari, Chief, Spots, and the other dogs return to the city to prove that the canine flu works, while an exchange student, Tracy Walker, has rounded up her classmates to expose Kobayashi's crimes. Thanks to Atari, Kobayashi has a change of heart and undoes the decree. After an incident involving a robot dog, Atari and Spots are both injured, so Kobayashi donates a kidney to Atari, while Spots gets a new eye.
The dogs return to their owners, and Kobayashi and his people are sent to jail. Atari becomes the new mayor of Megasaki, and he starts a relationship with Tracy, while Chief and Tracy's dog Nutmeg start to get closer. Spots ends up raising his family in the Kobayashi manor.
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