The film starts with a family going on a trip through the mountains. Little Pete (Levi Alexander) is reading a book about a puppy named Elliot. A deer runs into the road and causes Pete's dad to swerve the car, causing an accident that kills Pete's parents. Pete wanders out of the car and into the woods all alone. A pack of wolves come out and surround Pete, but they are scared off by the appearance of a large dragon. Pete asks the dragon if he is going to eat him. The dragon gently approaches Pete. The boy touches him, and the dragon's fur turns green. He takes Elliot in his paw and flies away with him.
It is now six years later. Mr. Meacham (Robert Redford) is telling a group of kids a story about the dragon that lives in the woods. His daughter Grace (Bryce Dallas Howard), a park ranger, listens in on the story.
Pete (now played by Oakes Fegley) lives with Elliot in the woods now. Pete catches a rabbit, but a bear lurks behind him. The bear runs away once Elliot shows up. Together, Pete and Elliot fly above the woods. Elliot also has the ability to turn invisible. At night, they sleep in a cave.
Grace is going through the woods doing her job while Pete observes her from a hiding place. When she's not looking, Pete sneaks by and takes a compass locket out of her bag. Grace thinks she hears something in the woods, but she sees nothing and leaves.
A group of lumberjacks led by Gavin (Karl Urban) are working in the woods, chopping down some trees. Gavin's brother Jack (Wes Bentley), also Grace's fiance, shows up along with his daughter Natalie (Oona Laurence), while Grace arrives on the scene. None of them are happy that Gavin is cutting down trees on his own accord. Natalie then sees Pete in the woods and follows him. Pete climbs a tree, and Natalie does the same. She slips and almost falls, but Pete catches her, causing them both to fall. They land on a branch and Pete hangs onto her, but Natalie drops a few feet and gets a scrape. The adults come running by and they discover Pete. He runs away, but Gavin catches him as he tries climbing up another tree. Pete falls and bumps his head, knocking himself out. Elliot then awakens as if to sense something is wrong. He lets out a low groaning sound, which Gavin hears.
Pete wakes up in the hospital. As the doctors are telling Grace that he's fine, he escapes out the window. Pete runs into the streets, going as far as to climb a schoolbus and hop onto another car. He is eventually found by Sheriff Dentler (Isiah Whitlock, Jr), along with Grace and Natalie. They take him in.
At night, Gavin and his mates go into the woods, armed. Elliot lurks by in camouflage. The men find Pete and Elliot's hideout, causing Elliot to reveal himself. He swipes Gavin's gun as the men make a run for it. Elliot then sneezes on Gavin and gets snot all over him. The men flee the scene.
Grace brings Pete back to her home. He tries running away again, but Grace promises to take him back to the woods if he just stays the night. Pete is given a real meal for the first time in ages. He tells Natalie about Elliot, which Grace overhears and recognizes as the same dragon her dad told her stories about. Grace then gets a call from the Sheriff, who says that they found records of Pete's family having gone missing. Meanwhile, Elliot flies around town and is spotted by people near the hospital. He eventually comes across Grace's home and sees that Elliot is doing okay. He flies back to his cave.
The next day, Pete guides Grace, Natalie, and Mr. Meacham into the woods to find Elliot. The dragon becomes visible, to the astonishment of everyone. Moments later, Gavin and his men come in and tranquilize Elliot before capturing him.
The men keep Elliot sedated and locked up in a warehouse. Pete and Natalie attempt to set him free through the skylight. Gavin brings the Sheriff and other townsfolk to see Elliot, but when they enter the warehouse, he is nowhere to be found. Gavin thinks he flew out, but Elliot is just invisible while Pete and Natalie are hiding in the truck, which Grace notices. Mr. Meacham arrives and helps the kids break out of the warehouse. Elliot is exposed, and everyone begins to chase after them.
The whole police squad pursues Elliot, Mr. Meacham and the kids. Elliot is still too weak to fly, and his attempt causes him to fall hard on the truck and cut off the brake line. Gavin tries to get Mr. Meacham to pull over, but he refuses. Gavin drives up ahead and tries to get them to stop before the bridge. Mr. Meacham is unable to pull the brakes, causing him to slam into Gavin's truck as the men run away. Mr. Meacham pulls the emergency brakes and stops at the end of the bridge. The police are coming in closer. Elliot is now angry, and he runs to the top of the bridge. Pete pleads with him not to do what he's about to do, but Elliot breathes fire down on the bridge to stop the police from advancing. Grace and Jack come by in their truck and halt before the fire gets them. The fire breaks through the bridge and causes the truck to start falling. Gavin attempts to rescue Grace and Jack as Jack breaks the glass in the back. The bridge starts breaking, causing the truck to plummet down along with Elliot. After a tense moment, Elliot flies up with Grace and Jack riding on his back. He brings them to safety, and then flies away with Pete.
Pete and Elliot return to their part of the woods. A tree has fallen over their cave, leaving them with nowhere to stay. Pete knows this means they cannot stay there anymore, and it also means they have to leave each other. Pete hugs Elliot, and the dragon comforts the boy. Pete is brought back to Grace, Jack, and Natalie, while Elliot flies away.
Sometime later, Grace and Jack have gotten married and have adopted Pete. Mr. Meacham's voice is heard saying that nobody ever saw Elliot again, and he hasn't told a story about him since. Gavin has given up looking for Elliot and goes back to work. Pete and his new family then take a trip to the mountains. Pete reunites with Elliot and sees that he is now with five other dragons. The family watches as the dragons fly away together.
*CUT TO THE CHASE*
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Pete's parents die in a car accident, so he lives with Elliot the dragon for six years before being found by Grace Meacham and her soon-to-be-stepdaughter Natalie. They take Pete in to give him a real home. Elliot flies around town and sees this, knowing he is better off.
When Pete tries to show Elliot to Grace, Natalie, and Grace's father, Elliot gets captured by Natalie's uncle Gavin and his men. Mr. Meacham helps the kids break Elliot out, leading to a climax on a bridge where Elliot wrecks a bridge by breathing fire to keep the police away. Grace and Jack (her fiance and Natalie's dad) fall through the bridge with Elliot, but the dragon saves them.
Pete and Elliot have to part ways when their cave is destroyed, and Elliot knows Pete must have a real family. Grace and Jack get married and adopt Pete, while Elliot finds his own family of dragons.
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