Arlo Beauregard, a unique boy born of both human and alligator lineage, embarks on an extraordinary journey that begins when he is abandoned shortly after birth and swept away through a sewage drain into the ocean. He finds refuge in a swamp, where he is lovingly adopted and raised by Edmée. As Arlo reaches his teenage years, a longing to connect with the world beyond his swamp home grows, yet he grapples with the fear that his alligator appearance will lead to rejection from society.
On his fifteenth birthday, Edmée presents Arlo with his birth wristband, sharing the revelation of his origin from New York City. Unknown to him, he had been abandoned, prompting Arlo to embark on a quest to find his biological father, Ansel Beauregard.
During his travels, Arlo is spotted by a passerby who alerts two alligator hunters, Ruff and Stucky, to capture him using a fearsome creature known as "the Beast." Just as the hunters close in, Arlo is rescued by a fellow teenager named Bertie. Together, they venture into a wrestling club where they encounter Furlecia, Teeny Tiny Tony, and Alia, who pledge their support to help Arlo and Bertie reach New York City, provided they assist in rescuing their friend Marcellus from an aquarium.
Upon their arrival in the bustling metropolis, they soon spot Ansel Beauregard, an entrepreneur with ambitious plans to reconstruct parts of the coastal city. In an effort to communicate with him, Arlo separates from his companions but is crushed when Ansel informs him he is not his son. Stubbornly, Arlo disputes this claim, only for Ansel to suggest changes to Arlo's appearance in a bid to fit in, leaving Arlo shocked and disheartened. Seeking solace, Arlo retreats into a sewage drain, where his loyal friends eventually find him at the development site of Ansel's project. They impart the valuable lesson that it is alright to be different and that one’s imperfections are what truly define them.
Later that evening, in a daring escapade at the Met Gala, Arlo and his friends infiltrate the event but are pursued by Ruff, Stucky, and the Beast. As Arlo disrupts the gala, Ansel attempts to communicate his truths. However, the tension escalates as Arlo falls into the grasps of Ruff and Stucky. With a daring rescue, Ansel reveals that he is indeed Arlo’s father and, like Arlo, carries the unique identity of being half-bird. Ansel confesses he gave Arlo up to protect him from the challenges of being different and begs for forgiveness to rebuild their father-son bond. Overjoyed, Arlo embraces Ansel and forgives him while choosing to remain with his friends, officially bringing Bertie into their circle.
In a heartwarming conclusion, Ansel decides to let the group revitalize the seashore area of the city in its original splendor, affirming Arlo's newfound sense of belonging.
In a poignant mid-credits scene, Edmée receives a postcard that shares the news of Arlo's fulfilling life, a testament to the love and connection that transcends distance.
