The movie begins in a pet store, where a group of puppies are playing in a pen. All the puppies are following each other and moving in a pack, except for one white one, who's playing with a squeaky carrot toy. A little girl comes into the store and buys the white puppy, giving it a collar with the nametag 'Bolt'.
Five years later, the girl, Penny (Miley Cyrus) and Bolt (John Travolta) are in the park, when Penny recieves a phone call from her father telling her that "something's come up at work" and he won't be around for a while. As he warns Penny not to go back to the house, the evil Dr. Calico (Malcolm McDowell) sneaks up on him.
Before he's interrupted, Penny's father tells her not to worry, that Bolt will protect her. A clip-montage plays, showing that her father (a scientist) has genetically altered Bolt, giving him a variety of super-powers, as well as the distinctive black lightning-bolt mark on his flank.
Back to the story, Penny is using a pair of enhanced binoculars to spy on one of Dr. Calico's associates, who is speaking to him via a hologram video. Dr. Calico says that he knows how to make Penny's father reveal his secrets, and that they just need to find a "certain thing" first. Calico's associate leaves the building, and Penny and Bolt follow at a distance.
They follow him down an alleyway, at which point he disappears...and then a car comes racing towards them. Bolt runs ahead and when the car hits him, it's flung over his head and lands upside-down behind him. Calico's associate is still alive, but trapped in the car, and Penny has Bolt hold the car (with his teeth) over the side of a bridge in order to make him tell them where Calico is.
Calico is evidently in Bolivia, but by now they've been found again. Penny pulls out a fold-out scooter and zooms off down the highway, with Bolt running by her side, as a group of helicopters and motorcycling bad guys (armed with electrified gloves) chase them. Using her helmet computer, she sees that there's a flight about to leave for Bolivia, and so they head towards the airport.
During the chase, Bolt uses his various superpowers to defeat the bad guys; he uses super-jumps to leap around, laser eyes to blow up the helicopters, and super-speed to pull Penny away from them. (She tells him to use the 'zoom-zoom' trick, where he grabs onto a piece of rope and pulls her scooter at hyperspeeds down the highway.) One of the bad guys pulls out a bomb shaped like a frisbee and attaches it to a gas tanker driving next to a schoolbus; Penny tells Bolt to 'fetch', so he leaves her briefly and pulls the bomb off, leaving it on a bad guy's head. The bad guy freaks out and throws it upwards, accidentally destroying the last helicopter, and when he realizes what he's done he slaps himself on the forehead...with his electrified glove.
With all the bad guys dispatched, Penny and Bolt continue on to the airport, but before they get far they're confronted with an army of Calico's forces: helicopters, tanks, cars, etc., that go on for miles. Penny tells Bolt to "speak" and Bolt braces himself, then lets loose with his super-bark: a supersonic boom that literally blows away the entire army.
After Bolt has defeated the army, Penny picks him up and takes a picture with him on her camera, laughing him and telling him "you're my good boy". She walks off to the side and enters a trailer with Bolt's name on the side; after the door has closed, all the bad guys get up, the background lifts up and people start clearing away the wreckage, revealing the whole thing was actually just a movie set.
We cut to the director going through the footage from the day's shooting. Everything is going fine until they get to one shot...and there's a boom mic visible in the background. The director flips out and starts screaming at the crew, yelling that "the dog could have seen it!". One of the people in the room asks why that's so important -- it turns out she's a representative from the network. The director tells her that in order to give the character emotional depth, they make sure that the dog thinks the entire show is real -- they hide all the cameras, use elaborate practical special effects, never re-shoot a scene, and most importantly: they never let Bolt off the set, EVER. Because Bolt loves Penny and really believes he's protecting her, it gives the show an edge an acting dog wouldn't -- as the director puts it, "If the dog believes it, the audience believes it."
Mindy, the network lady, isn't impressed. She says she doesn't care about the dog, but the show is getting too predictable, that audiences are getting tired of happy endings. She tells the director that if they lose so much as half a rating, everyone in the room (all the staff) will be fired.
Back in Bolt's trailer, Penny sticks up the photo she took on a wall, admist a group of other, similar photos. (Apparently she takes one whenever Bolt saves her.) Bolt is still freaking out because he thinks she's still in danger, so he just stands at the door and growls, in protect-mode. Penny tries to distract him, telling him she's fine and he already saved her, but nothing she does -- from feeding him to enticing him with toys, including his old squeaky carrot -- gets him to move away from the door. Finally Penny's cell phone rings and she has to leave, locking Bolt inside the trailer as she goes.
Outside the trailer, Penny's (real) mother and her agent meet her, flanked by a group of other staff members (her bodyguard, wardrobe artist, etc). Penny asks her agent if she can take Bolt home for the weekend -- the agent, who is really annoying, gives her a lot of roundabout talk and finally says no, because Bolt is never allowed off the set. Penny protests that Bolt never gets a chance to be a "real dog", but her agent feeds her a line about sticking a pin in it and hanging it up for later thought. Then they leave the set.
A little later, two of Dr. Calico's pet cats wander in. One of the cats is new, so the other cat is telling him how Bolt believes it's all real, and they like to torment him by playing along. They jump on top of Bolt's trailer, open the sunroof and taunt him, telling him that even though he and Penny have escaped "this time", they'll be back. Bolt tells them that he would super-bark them away, except he needs them to pass a message onto Calico (a generic "you'll never get away with it"-type thing). The cats taunt him a little more, then as they walk off again, the new cat tells Bolt that he's a huge fan and loves his work.
The next day, back in the show, Penny and Bolt are sneaking into Dr. Calico's lair to try and rescue her father. This time we see how all the cameras are hidden, and how they do some of the special effects -- there's a camera underneath the truck that they sneak in on, and the bad guys that Bolt defeats are just throwing themselves backwards onto stunt cushions. Some of the props are rigged to bend or explode when Bolt thinks he's using his powers on them. It's obvious that the staff has gotten very good at timing things exactly right, so that Bolt never figures it out.
They sneak into the computer room, and Bolt knocks out the guard at the computer with a karate-chop to the neck. Penny gets on the computer and tries to use it to find her father, but Dr. Calico (and his cats) interrupt -- the whole thing was actually a trap. The computer chair turns into a capsule, trapping Penny inside, and she's lifted away as Bolt watches helplessly. He tries to run after her, but a staff member in protective gear grabs him and pulls him back, stuffing him into a cage.
As he's being dragged away, Penny (now out of the fake capsule) tries to get near him, but the staff won't let her. She demands that they let her see him, because he thinks she's really in danger and doesn't understand that she's really okay. She isn't able to get through though, and he's taken back to his trailer. The staff member who lets him out of the cage tries to calm him down, but he's still freaking out.
Now that the take is over, Dr. Calico's cats decide to go torment Bolt some more. As they open up the sun roof, though, Bolt uses the staff member's head as a boost and jumps out of the trailer, knocking the cats away and escaping into the studio. He hears Penny calling for help -- actually a sound editor reviewing some footage -- and runs into a room with a lot of boxes to be shipped. He tries to break the window with his super-strength, but of course it doesn't work, and he only ends up knocking himself out. He falls into one of the boxes, and ends up being packed up by a staff member and shipped out.
He wakes up in on the other side of the country in New York, where the boxes have been delivered. The guy unpacking the boxes sees one of them moving and opens it, and Bolt jumps out at him, escaping out onto the streets of New York. He sees what he thinks is the capsule containing Penny -- actually a portable toilet with a symbol that looks like Calico's eye on it -- and follows it, knocking it off of the truck that's carrying it. When Penny's not inside, he decides that they must have moved her, and now he doesn't know where to look.
While he's in New York, Bolt tries to use his superpowers, but of course they don't work. He falls in the middle of his super-jumps, he can't break through a fence with his super-strength, and when he tries to knock out a man who looks like Calico from the back, he just taps him on the shoulder. He assumes he must've been weakened somehow by Calico, and he tries to recruit a group of dogs to help him; the dogs just laugh at him, though, and Bolt has no idea what they're talking about. The dog-walker sees him and attaches a leash to his collar, assuming he was part of her group that got lost, but he breaks away and runs off.
Next he meets a group of pigeons, who think they've seen him somewhere before, but can't remember where. (Even as two buses with giant ads for the Bolt TV show pass by.) They see that Bolt still has some of the styrofoam packing peanuts from the box he was in stuck to his fur; Bolt, who has never heard of styrofoam before, concludes that it must be some kind of evil substance that negates his superpowers. He decides that he needs to find someone close to Dr. Calico (whom he refers to as "the green-eyed man"), someone like...a cat. The pigeons seem to get an idea and tell him they know just where to find such a cat.
We cut to Mittens (Susie Essman), an alley cat who rules over the pigeons of New York. Every day they give her half of the food they find, in exchange for her protection. The pigeons are all presenting their food to her, but when one of them doesn't give enough, she tells him that tomorrow, he'll have to give her all of his food instead of half. When the pigeon protests, she tells him that her claws have a mind of their own, and when she gets hungry, her claws come out and she can't control them. The pigeon apologizes and begs her not to claw him, then tells her as he's leaving that one day, someone's going to stand up to her. Mittens laughs at him, and is then immediately tackled by Bolt, demanding that she bring him to Penny.
Mittens has no idea what he's talking about (although the pigeons tell Bolt that she's lying), so Bolt holds her over a bridge and threatens to drop her into traffic unless she gives him what he wants. Mittens thinks he's crazy and finally lies and says that she'll bring him to Penny, so he won't drop her. She sees a Hollywood address on the back of his collar tag and tells him that's where Penny is.
After Bolt ties her to his leash so that she can't escape, she goes into the dumpster behind a waffle restaurant and digs out one of those cheesy maps that show the restaurant locations in every state. She shows Bolt that they're on one end of the country (in New York), and Penny's on the other (in California). Bolt still won't let her go, though, not until he finds Penny; Mittens isn't happy about it, but she doesn't have a choice. She's dragged along when Bolt runs off, and ends up getting knocked out when she hits a mailbox. Meanwhile, the pigeons wonder if maybe they went too far, but since they're now free of Mittens, they don't care.
Bolt finds a truck that two guys are loading a sofa into, and he sneaks in by hiding himself and Mittens' unconscious body underneath the sofa. By the time Mittens wakes up, they're on the move.
Mittens obviously doesn't believe that Bolt has superpowers, and just thinks he's crazy, but she's bored during the ride and asks what kind of powers he has while she digs through the stuff in the moving van. Bolt won't tell her, but Mittens notices a baseball bat in one of the boxes, and keeps asking to keep him talking while she works it out of the box. Finally Bolt admits that he has a super-bark, as Mittens is about to hit him with the bat, but it's too heavy for her and she crashes into a stack of boxes, sending one of them down onto Bolt's head. It doesn't hurt him, but it's filled with styrofoam peanuts, and Bolt freaks out, jumping out of the moving truck and rolling down a hill. Mittens is dragged along behind him.
Bolt is surprised that the landing hurt, because he's "usually more invulnerable". His paw is bleeding, although he doesn't know what that means. Mittens threatens him with a styrofoam peanut that fell out of the truck with them, but he distracts her by saying "that's an odd place for a piano" and knocks it away. Suddenly his stomach growls, and he freaks out again, thinking that Mittens has poisoned him. Since he was always fed regularly at the studio, he's never really been hungry before. Mittens is surprised that he doesn't know what it's like to bleed or be hungry, although Bolt still thinks she's poisoned him, and demands the antidote.
Mittens says that the antidote is food, so they find an RV rest stop where a bunch of RVs are parked, with families picnicking and grilling burgers. Mittens teaches Bolt how to beg, so that when the families look out of their RVs and see him, they throw food for the cute doggie. (Mittens tries it too, but when she does it, she gets a pan thrown at her.)
One of the RVs is owned by a little old lady who has a bunch of pet hamsters. Most of them are in cages, but one of them is out in an exercise ball, leaning on the remote and flipping through the channels on the TV. When the old lady leaves to get some food for Bolt, the hamster recognizes him, and rolls out of the trailer to follow them.
The hamster introduces himself as Rhino (Mark Walton) and is totally excited to be meeting Bolt, whom he says is his hero. He even has a little dark patch vaguely shaped like a lightning bolt, which he thinks makes them like twins. Mittens is astonished that he actually knows of Bolt, and even more astonished when Bolt says that Rhino can come along with them. Not only because Rhino is an overly-excited idiot, but because she can't believe they want to leave the RV park. She thinks they should stay, because new RVs will be coming through all the time, and they'll have a good place to sleep and a steady supply of food. She doesn't understand why Bolt is so hung up on saving Penny. Bolt says that Penny is his person, and Mittens just scoffs at the idea.
Back in Hollywood, Penny is disraught over Bolt's disappearance. She says he must be so scared, but her mom hugs her and says that Bolt isn't afraid of anything, and he'll definitely come back. Then Penny's agent comes in and says he has good news -- Penny thinks they've found Bolt, but it's really just that she's gotten a spot as the lead guest on The Tonight Show. Penny doesn't care and doesn't want to go on the show, much to her agent's horror.
Meanwhile, Bolt and Rhino decide that they're going to hop on a train by jumping on it as it passes underneath a bridge, although Mittens is convinced that they're all going to be killed. Bolt plans on using a banner hung up on the bridge to swing onto the train, and they can then ride it much faster than a car would take them. Rhino is all excited as they're about to jump, and says that it was really cool when he did "on the magic box". Mittens starts to realize what's going on and asks if the "magic box" had moving pictures on it, and Rhino says yes, and that Bolt's pictures were the best. Mittens realizes that Bolt is just a TV dog right as they jump down, and of course, it doesn't work out the way Bolt had planned it -- they miss the train at first, then crash into it when they swing back and nearly fall off. Bolt and Rhino are seperated but make it to the top, but Mittens grabs onto a ladder on the back of the train. She can't hold on very well, so Bolt tries to pull her up, although she just screams at him that he doesn't really have superpowers.
They end up both falling on the ladder, which falls down, leaving Bolt suspended over the moving tracks. His leash is caught and he can't pull free, and there's a small building up ahead that he'll crash into if he doesn't move. Mittens, who's climbed onto the train, sees that the screws holding the ladder onto the train are coming loose. The leash is still holding her onto Bolt, so naturally, she tries to save him by holding the screws down. Rhino finds them just then, and thinks that Mittens is trying to unscrew the ladder instead of holding it on. He starts pushing her away, ignoring her when she protests, but then she sees that the other screw on the ladder is coming out. When she tries to hold that down, too, the other one comes loose, and they only barely escape getting smashed as Bolt's leash comes loose and they fall off the train.
They make their way to a suburb, where Mittens climbs a tree and Bolt barks at her. Mittens is disdainful now that she knows the truth about Bolt, and when he doesn't believe her, tells him to go ahead and blow her away with a super-bark. Bolt braces himself, getting into his super-bark pose, and he lets loose with a big one...which does nothing. Confused, he tries again and again, as Mittens makes sarcastic remarks from the tree branch above.
Suddenly Mittens a truck coming, and she tells Bolt to shut up because they have to run. Bolt keeps barking though, and the truck sees them -- it's animal control, and they grab Bolt and Mittens and put them in the truck to take them to the animal shelter. Rhino escapes their notice, though.
In the truck, Bolt and Mittens are separated and put in cages next to each other. (The cages are built into the truck, and there are latches on both the inside and outside of the truck.) They can't see each other, though. Bolt makes numerous attempts to escape, including staring at the lock and trying to melt it with his laser-eyes. (Since none of his powers work, he deduces that the truck must be made of styrofoam.) He ignores Mittens when she tries again to tell him that he doesn't really have superpowers, and that even his lightning-bolt mark isn't real, it's just make-up. Mittens tells him that what's going to happen is that they're going to the shelter, where Bolt will end up being adopted, but she'll be there forever, because she's not cute like he is. Bolt refuses to give up and keeps trying to bash his way outside with his head.
Meanwhile, Rhino figures out how to open his ball from the inside, and he sets off after them. He jumps on when the truck stops for gas, and as Bolt continues trying to bash his way out, he starts pulling at the lock. He finally gets it free just as Bolt runs at the door again and it breaks open, tossing both him and Rhino out into a nearby field. Bolt is ecstatic at this proof that his powers really do work...until he notices Rhino, who tells him that he opened the lock from the outside.
Bolt suddenly realizes that Mittens was right all along, and he doesn't really have any powers. He runs his paw along his lightning-bolt mark, and the make-up comes off on his paw. Dejected, he realizes he can't really do anything after all. Rhino, astonished at his hero's doubt in himself, makes a speech telling Bolt that he's a hero to all animals who think they can't do anything, and that right now Mittens needs him to be a hero for her. After a little more convincing, Bolt decides that even though he's not really a superhero, he still has to do what he can for Mittens and Penny. Rhino is pleased that Bolt isn't giving up, and goes to get his ball.
Bolt and Rhino (now in the ball again) follow the truck to the shelter, where they make a plan to sneak in. Rhino wants to do it just like an episode of Bolt's TV show, but Bolt -- now that he knows it won't work that way in real life -- decides they should be more stealthy. Rhino gets so excited that his breath fogs up the inside of his ball (and he draws a smiley-face on the glass with his finger).
One of the guards, Lloyd, is just leaving, and he says goodnight to Esther, another guard who is watching the door. (According to a banner on the wall, it is Adopt-a-Pet week.) After he leaves, Bolt and Rhino go in; when Esther hears the automatic doors open, she thinks Lloyd is going to jump out at her and scare her, and she threatens to pepper-spray him "again". She grabs a flashlight and goes off to look for him, intent on catching him in the act, and Bolt and Rhino take the opportunity to sneak into the back.
In the back, there are two (conveniently already open) doors -- one marked with a picture of a dog, and one with a picture of a cat, both watched by a guard. Rhino offers to snap the guard's neck, but Bolt instead tosses him into the dog area...where all the dogs immediately perk up and start barking at the "ball". When the guard goes to investigate, Bolt sneaks into the cat area.
Mittens is curled up in a small cage, resigned to her fate, and can't believe it when Bolt shows up. Bolt tells her that she was right and he doesn't have superpowers, and she's surprised that he came back for her anyway. He asks her if she's ready for this, and she says no, and he says he isn't either.
He's able to lift the latch on her cage and they run out, just as the guard finds the dogs slobbering all over Rhino's ball, and one of them trying to chew on it. Bolt barks to let Rhino know it's time to escape, and the guard turns around to chase them, but ends up tripping over his own feet. Rhino shoots out of the dog's mouth and whangs the guard in the head, rolling off after Bolt and Mittens. They head towards the automatic doors, but Lloyd is standing in front of them; the guard yells at him to lock the door, and Bolt and Mittens skid to a stop as he blocks their way. Rhino yells at Bolt to use his super-bark.
The guard coming up behind them slips on the trail of dog drool that Rhino's ball left behind, and accidentally kicks Rhino (and steps on Bolt's tail); as Bolt lets out a surprised bark, Rhino bounces off of Lloyd's head, knocking him over, and hits a can of helium that was being used to blow up the balloons for Adopt-a-Pet week. The can shoots around the room, powered by the helium leaking out of the end, and out the door, right over Lloyd -- and right into the big sign in the parking lot for the animal shelter. The sign falls over onto a truck, causing a huge explosion, and the three animals make their getaway admist the flaming wreckage. Meanwhile, Esther is horrified to see what's happened to her truck -- and as the hapless guard runs out and trips over Lloyd's unconscious body, she pepper-sprays him in the face.
Meanwhile, the animals make it to a highway, and Bolt and Mittens have a somewhat awkward reconciliation. Bolt still wants to go to California, because once again, Penny is his person and he has to protect her. Mittens still doesn't understand, but is now willing to go along with him anyway, although they still need transportation. Just then Rhino notices a truck transporting a house, so they hop aboard as it goes by.
Inside the house, Mittens decides that Bolt should learn how to be a regular dog, one who knows how to beg and play with toys. She says that the reason cats hate dogs so much is because all cats have a "dog complex" -- dogs have such great lives that all cats secretly want to be dogs, and it's not fair that he doesn't get to enjoy it. So she shows him stuff like the toilet (Bolt can't believe he's supposed to drink out of it), the kitchen (where the entire floor is his dogbowl), and the fireplace. Meanwhile, Rhino is playing around with a vent, talking into one end and having his voice come out on the other side of the house, and thoroughly annoying them in the process.
Bolt thinks Mittens knows a lot about this sort of thing, and Mittens reveals that she used to have owners, but says she got tired of being owned and left when she got bored with them. Then she changes the subject by having Bolt stick his head out the window and let his tongue hang out. Bolt says that it's awesome and that she should try it, but she says it's more of a dog thing.
There's another clip-montage here, showing their travels across the country, following the waffle map. They work out a system: whenever the truck they're on starts to go a different way, they get off, and find a new one going the right direction. They eat out of dumpsters and track their progress by finding the waffle restaurants in each state; in this way, they make their way slowly across the country. In the meantime, Mittens is teaching Bolt about how to be a real dog; she teaches him how to fetch, how to play with other dogs they meet, and everything else he's been missing this whole time. Bolt is getting more excited about finding Penny now, and realizes that he wants to be her dog instead of just her protector.
Meanwhile, Penny and her mom are photocopying a bunch of 'lost dog' posters with Bolt's picture on them. Penny's agent comes in saying they've found Bolt -- Penny is excited at first, but when they bring out the dog, she realizes it isn't Bolt, it's a trained acting dog that just looks like him. At first she refuses to work with the new dog, especially after her agent tells her an incomprehensible story about getting a baseball glove instead of the bike he wanted for Christmas ("So I just pretended the glove was a bike, and rode it to school every day! True story!"), but then Mindy the network lady comes in and explains to her that she needs to move on. Penny decides that she's right and presses the 'stop' button on the photocopier.
By now, the animals have reached Las Vegas, and are having the time of their lives. At one point Mittens disappears for a while, then comes back and says she wants to show Bolt something. She leads him to a pile of junk, where she's set up some cardboard boxes -- one for her and one for him. His even has a soft cushion that she stuffed with styrofoam (for irony), and he can let the box flaps down whenever he wants some privacy.
Bolt is surprised that Mittens wants to stay, and Mittens is equally surprised that Bolt doesn't. Bolt still insists that he has to find Penny, so Mittens drags him (by the ear) out to where they can see a giant billboard advertising his TV show. She says that she's real, that THIS is real, and that the stuff on the billboard isn't. That Penny doesn't really love him, she's just an actress doing her job. Bolt refuses to believe it, and Mittens gets angry, saying that humans don't really care about them. She gets angry enough that she reveals that she didn't leave her owners by choice -- they just abandoned her one day, leaving her to fend for herself. It also comes out that Mittens is declawed. Bolt feels sorry for her, but he still insists that he needs to get back home. Mittens says she's sorry she ever took pity on him, and Bolt leaves. He hops on the back of a truck and heads off to Hollywood, still feeling bad about leaving his friends, but knowing he has to find Penny no matter what.
Meanwhile, Rhino finds Mittens, and asks where Bolt went. Mittens doesn't have the heart to tell him what really happened, so instead she tells him that Bolt said he needed to go fight "the green-eyed man" alone. Rhino starts to go after him, and when Mittens asks why, he says that it's because you don't ever abandon your friends, no matter what they say. Mittens tells him he's going in the wrong direction, and Rhino turns around and starts heading off again. Mittens decides she can't abandon Bolt after all and goes with him.
Back with Bolt, he's finally reached Hollywood, jumping off the truck when the driver stops to take a picture of the Hollywood sign. As he starts down into the city, he's accosted by three pigeons -- but unlike the New York pigeons, these are ambitious writer-wannabe pigeons, who recognize him and try to pitch him an idea for the show. (The third pigeon, obviously a hapless lackey, is sent off to get them some crumbs -- "whole wheat, not multigrain, whole wheat is not the same thing as multigrain!"). They tell him that they think the show should have Penny being abducted by aliens. Bolt gets an idea and says that if they help him find Penny, he'd love to listen to more of their pitch on the way. The pigeons agree and lead him off to the studio while talking more about their alien idea.
Meanwhile, Mittens and Rhino have also reached Hollywood, and they also head towards the studio to find Bolt. As they enter the studio, Rhino notices one of the actors who plays Dr. Calico's henchmen, standing in-costume outside the set. He rolls up and attempts to "defeat" him by pushing against his leg; the actor sees him and picks him up, cooing over what an adorable hamster he is.
Bolt manages to get into the studio without being noticed, and even gets on-set and finds his trailer again. (By this time his fur is matted and dirty, and his lightning-bolt is almost rubbed all the way off.) He's excited to see his home again, and starts playing with his old squeaky carrot. Suddenly he hears Penny's voice, and with the carrot in his mouth, he runs off; he can see her at the end of a hallway, calling his name but not looking at him, and he runs towards her, happy to finally have found his person again. As he's almost at the end of the hallway, though, the trained dog runs into view, leaping into Penny's arms. Penny laughs and says "you're my good boy". Broken-hearted, Bolt slinks back into the shadows before Penny can see him, and turns and leaves.
Just as he leaves, the trained dog jumps out of Penny's arms and runs to his trainer, who's his real master -- the whole thing was just a rehearsal for an episode. Penny looks upset and hugs her mom, saying that she still misses Bolt. Up in the rafters, Mittens is standing, having seen the whole thing.
The TV crew sets up Dr. Calico's lair, hoisting Penny up on a harness and making it look like she's tied up and hung from a rope. The set is dark and spooky, with lots of lit torches and fire effects. They start to film the scene.
In the scene, Penny's father is taken into the lair, where Dr. Calico thanks him in advance for revealing his secret scientific research to them. When he says he'll never give them his research, Dr. Calico shows him that he's captured Penny, and will kill her if he doesn't comply. Penny calls for Bolt -- and the trained dog smashes through the fake doorway, growling. When Dr. Calico calls for his henchmen, though, the dog gets scared of their electrified gloves and runs away, accidentally knocking over some of the torches. The set catches fire and all the of the crew panics, running over each other in an attempt to evacuate. In the confusion, no one notices Penny -- still in her harness -- calling for help.
Mittens catches up with Bolt as he's leaving the studio; so does Rhino, who was released when the actor noticed the set was on fire. Bolt says that Mittens was right all along, but Mittens says that she was wrong, and that Penny hasn't given up on him. She says that the look on Penny's face when he left was broken-hearted. Bolt tells her to be quiet, and she gets angry, but Bolt says he didn't mean it like that -- he can hear Penny calling for help from the studio. He runs back, intent on saving her.
Back in the studio, everyone has evacuated except for Penny. She's managed to take off the fake rope effect, and presses the emergency release on her harness, dropping her to the ground. The room is all smoky now and there's debris everywhere from the ruined set, and she can't see where she's going.
The animals rush back to the studio, where they find an open door. There's a piece of debris falling right in front of it -- Rhino rolls his ball in just as it falls, propping it up and leaving just enough room for Bolt to slide in underneath. Mittens opens the ball and pulls Rhino out, just as the ball shatters under the weight and the debris falls the rest of the way down, blocking the exit.
Both Bolt and Penny run through the still-flaming set, until finally they find each other. Penny can't believe it's really Bolt, and is overjoyed that he's really come back to her. They don't have much time to rejoice, though, because the building is still on fire, and Penny is weak from smoke inhalation. She grabs a piece of rope and tells Bolt to use the 'zoom-zoom' trick; Bolt grabs onto the other end and uses it to guide her through the maze of wreckage. He finds an open vent that he can fit into that will take them outside, but Penny is too weak, and collapses. She tells Bolt to run away, but he goes over and sits by her side, not willing to leave without her.
Outside, Penny's mom is looking everywhere for her, and no one seems to be sure if she got out of the building or not. The firemen are spraying the fire and trying to contain it, assuming that everyone is outside already.
Inside the building, Bolt has almost given up hope when he remembers the trick that Rhino did with the vent, back when they were in the moving house. He braces himself, gets into his 'super-bark' pose, and barks as loudly as he can into the vent.
Penny's mother hears the bark from outside, coming from the vent. She makes everyone be quiet, and they hear Bolt bark again, proving that they're still inside. The firemen rush in to rescue the two of them as Rhino proudly says that that was a REAL super-bark.
Penny is put on a stretcher and loaded into an ambulance, although the EMT says that she'll probably be fine, but they're going to take her to the hospital just in case. Bolt is allowed to curl up next to her on the stretcher. Penny's agent weasels his way into the ambulance and starts worrying about how this will affect her career...so Penny's mom throws him out (literally) and tells him that they quit. The agent tries to beg them to reconsider as the ambulance zooms off.
The next scene is in a hospital bed, where a girl sits with bandages all over her face. The doctors say that the damage was worse than they had expected, and they had to rebuild her entire face -- they peel off the bandages, and it's a girl who sort of resembles Penny, with a similar haircut. It's obviously a new actress brought onto the show now that Penny's left. The new girl looks in a mirror and says that at least Calico won't recognize her now...but one of the nurses picks up a syringe and lunges at her with it, turning out to be Dr. Calico in disguise. Suddenly a blast of laser-vision knocks the syringe from Calico's hand, just as Bolt -- actually the trained acting dog -- smashes through the hospital window. He and the new girl jump out the window...only to be caught in the tractor beam of a UFO! A group of UFOs are shown zooming off into the night sky, as Calico shakes his fist and screams, "Aliens!"
The screen goes black, and we see that it was actually a TV screen that Rhino has just turned off in disgust, calling it "stupid". He, Mittens, and Bolt have now moved in with Penny and her mom -- Bolt is no longer a TV star, and instead gets to be a real dog all the time. Penny takes a picture of them all on the couch with her camera.
The movie ends with a group of pigeons on the front porch; one of them says that "that dog" looks familiar, and asks if they've seen him before. Another one says, "Nope, never seen his face before." and they fly off.
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