The central conspiracy of Isle of Dogs is that the canine flu outbreak was deliberately engineered by Mayor Kobayashi and his party. His anti-dog agenda is not a matter of public safety but the culmination of his cat-loving ancestors' long-held grudge against dogs. Professor Watanabe, who creates a cure for the flu, is assassinated with poisoned wasabi to suppress the truth.
A significant plot twist is the revelation of Chief's true identity. When Atari gives him a bath, his dirty fur is washed away to reveal a white and black-spotted coat, identical to Spots. This reveals they are from the same rare, expensive breed, foreshadowing their connection. The most crucial twist comes when the pack finally finds Spots. He is not a captive but the leader of a lost tribe of dogs who were the original test subjects at a secret lab on the island. Spots reveals that he is Chief's older brother, whom Chief had long thought was dead. Furthermore, Spots is now a father-to-be and relinquishes his duty as Atari's bodyguard to Chief, completing Chief's character arc from a lone stray to a devoted protector.
In the final confrontation, Tracy Walker and the student activists present evidence of Kobayashi's corruption. Moved by Atari's haiku, Kobayashi has a change of heart and rescinds the extermination order. His aide, Major Domo, attempts to proceed with the extermination anyway, but a student hacker foils the plan, causing the poison to backfire on the dog-catchers. In the ensuing chaos, Atari is critically injured and needs a kidney transplant. In a final act of redemption, Kobayashi donates his own kidney to save his nephew. Ultimately, Kobayashi and his conspirators are jailed, and Atari becomes the new mayor of Megasaki, reintegrating dogs into society.