In the prologue, a puppy named Bolt (John Travolta) is adopted by an seven-year-old girl named Penny (Miley Cyrus).
Five years later, they star on a hit adventurous television series called Bolt in which the titular character has various superpowers and must constantly thwart the evil plans of the nefarious Doctor Calico (Malcolm McDowell). To gain a more realistic performance, the TV show’s producers have deceived Bolt his entire life, arranging the filming in such a way that Bolt believes the television show is real and he really has superpowers, including a powerful sonic scream-like “superbark”. Mistakenly believing Penny has been kidnapped by the villain, Bolt escapes from his on-set trailer in Hollywood but bumps into a window and falls unconscious into a box of foam peanuts and unknown to the film company is accidentally shipped to New York City. In New York, Bolt eventually comes round, and starts to notice that his “superpowers” aren’t working, and rationalizes this is the effect that styrofoam has on his body. He then meets Mittens (Susie Essman), a female alley cat who bullies pigeons out of their food. Bolt (believing she’s one of Calico’s minions) forces Mittens to help him get back to Hollywood, and after Bolt knocks Mittens unconscious into a letter box, the two start their epic journey westward on a truck. In Hollywood, Penny is deeply saddened over Bolt’s disappearance but is convinced by the studio to continue filming with a Bolt lookalike.
Surprised at his first feelings of hunger, Bolt is shown by Mittens how to act like a cute, but needy dog, and is rewarded by food for the both of them at a nearby RV park, where they meet Rhino (Mark Walton), a fearless, TV-obsessed hamster and Bolt fan who joins their team. Rhino’s unwavering faith in Bolt substantiates the dog’s illusions about his superpowers, but Mittens, who has learned that Bolt is from a television show, tries to convince Bolt that his superpowers aren’t real. Bolt refuses to listen to Mittens, and instead becomes frustrated and attempts to “superbark” her repeatedly. The noise attracts Animal Control, who captures them both and transports them to an animal shelter. After being freed en route by Rhino, Bolt finally realizes that he is just a normal dog, but regains his confidence after Rhino (oblivious to this revelation) gives him a pep talk. They rescue Mittens from the shelter and escape, allowing them to continue their journey. Along the way, Mittens helps Bolt through his identity crisis by teaching him typical dog activities (such as hanging his head out car windows and chasing sticks), but Mittens refuses to go farther than Las Vegas. She tells Bolt that his Hollywood life is fake and there is no real love for him there. Her emotional rant reveals that she was once a house cat, but was abandoned by her previous owner and left to brave the harsh streets alone and declawed. Bolt refuses to believe that Penny doesn’t love him, and continues on alone, wishing Mittens the best. Rhino, learning of Bolt’s departure, convinces Mittens that they must help him, and the two set off to find Bolt once again.
Bolt reaches the studio and finds Penny embracing his lookalike. Unaware that Penny still misses him and that her affection for the lookalike is only a part of a rehearsal for the show, he leaves, brokenhearted. Mittens, on a gantry in the studio, sees what Bolt does not: Penny telling her mother how much she misses Bolt. Realizing that Penny truly does love Bolt, Mittens follows Bolt and explains. At the same time, the Bolt-lookalike panics during the show’s filming and accidentally knocks over some flaming torches, setting the sound stage on fire with Penny trapped inside. Bolt arrives and reunites with Penny inside the burning studio, but they cannot get out. In desperation, and unwilling to abandon Penny, Bolt uses his “superbark”. The firefighters hear the noise through the building’s air vent and manage to rescue them before they succumb to smoke inhalation.
Penny and her mother subsequently quit the show when their overeager agent attempts to exploit the incident for publicity purposes. Penny herself adopts Mittens and Rhino, and she and her family move to a rural home to enjoy a simpler, happy lifestyle with Bolt and her new pets. The show continues, but with a replacement “Bolt” and “Penny” – “Penny’s” new appearance being explained in the show as being serious injuries necessitating her undergoing facial reconstruction surgery, and adopting a new storyline about alien abduction (one that even Rhino finds unrealistic, and Bolt finds “ridonculous”). Ultimately, Bolt, Penny, her mother, Mittens, and Rhino are seen enjoying their new life together.