A small alien creature is accidentally launched into an escape pod and crashes onto Earth in the Mojave Desert in 1999, where a human scientist finds it. Fifteen years later, on his first birthday, Danny is given a puppy named Charlie as a birthday gift from his mother. Over the next decade, the two of them grow up together, with Charlie looking after Danny and forming a deep, loyal bond. But as Charlie ages, he experiences lethargy and health problems that keep him from playing with Danny the way he used to.
One night, an alien spaceship takes Charlie and, next door, the cat Puddy along. Charlie and Puddy are rounded up among several alien creatures chosen by an alien prince to be his pet. The prince is spoiled and harsh, and when he tries to discard the animals by throwing them out an airlock, his mother, the Alien Queen, is outraged by his selfishness and cruelty. She intervenes, returning Charlie and Puddy to Earth and making sure they are safe, and the prince loses his hope of a perfect pet.
The next morning, Danny discovers that Charlie can speak, is back to a younger, healthier self, and now possesses superpowers—flight, super strength, and keen senses. Puddy learns that he can also speak, has grown bigger, and now wields powers like telekinesis and high intelligence, which he uses to torment his owner, Otis. Before heading to school, Danny urges Charlie to stay under the radar, but Charlie’s new instincts pull him toward calls for help he can hear with his enhanced senses.
As Charlie begins to intervene, Danny realizes Charlie’s rescues are happening because of online videos showing his feats. After a conversation, Danny suggests that Charlie become a true superhero, nicknamed Wonderdog, and Charlie dons a mask and cape. That very night, he saves a bus from a sinkhole and becomes a sensation on the internet. He continues to answer emergencies—when he hears an airplane in danger, he helps land it safely.
Charlie’s rising profile draws attention from the President, the woman nicknamed the Madame President in the press, who wants to use Charlie to burnish her image and promote a new line of pet food. The plan works financially, driving other brands out of business as people flock to the Wonderdog product.
Meanwhile, Puddy grows bored with typical pet life and schemes to elevate his status. After the pet food branding becomes a problem, he hacks a satellite and targets the International Space Station. Charlie foils the plan and saves the station, but he nearly freezes in space and passes out, forcing Danny to wake him and steer him back to safety. The incident reveals that Puddy’s enhanced DNA experiments can affect other animals, and he begins dosing pet food to spread smarter, more capable cats that can challenge humans.
When a bomb threat is reported at a local museum, Charlie investigates and clears the crowd, even breaking into the vault to retrieve minerals he thinks are calling out for help. Unbeknownst to him, it’s a trap laid by Puddy, and Charlie is knocked out by knockout gas, framed for the theft by a loyal hench-cat called Cookie. Charlie is put on trial for grand larceny, and doctored security footage secures a guilty verdict, landing him under house arrest and turning public opinion against him. The President, frustrated by the money spent on Wonderdog, contemplates a profitable partnership with Puddy, who proposes relabeling the dog food as a cat-focused product and continuing to cash in on the brand’s momentum.
With Charlie out of the public eye, Danny begins to suspect that Puddy is orchestrating the whole scheme. He shares his evidence with Charlie, and the two realize that they must involve Danny’s mother and reveal Charlie’s true identity as Wonderdog. They discover a pendant connected to an alien ship and a beacon that leads to Puddy’s lair—a warehouse next to a shuttered amusement park. Together, Charlie and Danny confront the cat and his lackeys, aiming to stop the plan and reclaim Charlie’s good name.
A tense confrontation unfolds around the pendant, with Puddy threatening Danny to gain control of it. Danny defends Charlie by arguing that the hero’s strength comes from his heart and love for others, not from fear or anger. The two share a touching moment that reinforces Charlie’s resolve, and they realize the pendant has called in an alien ship. The queen emerges to demand the pendant’s origin, and Charlie’s mother explains how she once found part of one of the queen’s ships during the original incident with the alien creature.
The Queen’s son—the Alien Prince—intervenes, taking a strong interest in Puddy and using his telekinesis to bring the rebellious cat onto the ship, declaring his preference for Puddy as a pet. The Queen then uses her powers to restore Earth’s balance, returning humans, cats, and even Cookie to their normal selves and restoring Charlie’s youth and his health problems, though she initially questions whether the change should be permanent.
Moved by Charlie’s history of heroism and Danny’s sincere plea, the Queen telepathically witnesses the good Charlie has done and decides to make the transformation permanent. She bids them farewell and departs, leaving Earth to carry on with their new memory of Wonderdog.
Sometime later, life on Earth has improved. Otis has found a new love, Charlie has been cleared of the false charges and even has a hidden mission hub under his dog house, with Danny serving as his missions operator. The duo begins their first official joint mission, and Charlie heads out to save people from a hurricane, discovering that he now has heat vision to aid in the rescue. Their partnership marks the start of a new era of adventures, grounded in friendship, courage, and a steadfast belief in helping others, no matter the odds.
