After lightning strikes the clock tower and sends the Winnie the Pooh Goes Back to the Future Marty back to 1985, Marty McFly (Michael J. Fox), Winnie the Pooh, Piglet, Tigger, Rabbit, Eeyore, Kanga, Roo, Lumpy, Darby, Buster, Ash Ketchum, Pikachu, Misty, Brock, Togepi, Tennessee Tuxedo, and Chumley, who are stranded in 1955, take "Doc" Emmett Brown (Christopher Lloyd) home. They explain to the Doc of that era that Doc's future self and the DeLorean time machine were accidentally sent back to the year 1885. Marty, Pooh, Ash, Tennessee, and the other learn from a letter written by Doc in 1885, that the DeLorean is hidden in an old mineshaft. The letter instructs Marty, Pooh, Ash, and their friends to find the car, return to 1985, and then destroy it in order to prevent further disruption of the space-time continuum.
With the help of the Doc of 1955, Marty, Pooh, Ash, Tennessee, and the others retrieve the DeLorean. In the process, they discover a tombstone which leads them to learn that Doc was killed in 1885 by Buford "Mad Dog" Tannen, Nasty Jack, Cat R. Waul, Alameda Slim, and Team Rocket (Jessie, James, and Meowth), just seven days after having written the letter. Ignoring Doc's urging to return to 1985, Marty, Pooh, Ash, Tennessee, and their friends decide that they must save Doc, who had no idea he would be killed days later. Marty, Pooh, Ash, Tennessee, and the others take the DeLorean back to 1885, and arrive in the middle of a skirmish between a group of Native Americans and the United States cavalry, resulting in the DeLorean's fuel line being ruptured. After hiding the car, Marty, Pooh, Ash, Tennessee, and their friends trek towards town, encountering his great-great-grandparents who had recently arrived in America from Ireland. To mask his identity, he takes up the name "Clint Eastwood". After arriving in Hill Valley and nearly avoiding a skirmish with Shame, Buford, Nasty Jack, Cat R. Waul, Alameda Slim, and Team Rocket (Jessie, James, and Meowth), Marty, Pooh, Ash, Tennessee, and the others reunite with Doc, who agrees to leave when he learns of his upcoming fate. Doc sees Marty's photograph of his tombstone and concludes from the inscription that he was to have fallen in love with a woman named "Clara". Learning that the new schoolmarm he has promised to pick up is named Clara Clayton, Doc decides to leave without meeting her.
However, the ruptured fuel line has left the DeLorean's gas tank completely empty; and the DeLorean cannot reach 88 miles per hour without gasoline. After several failed attempts to accelerate the car through alternate means, Doc decides to push the DeLorean up to speed with a steam locomotive, but finds that the only track straight enough ends in an incomplete bridge over a deep ravine. The car will have to reach 88 miles per hour before reaching the bridge, so that it can travel to 1985 where the bridge is completed. As they scout the location, they save a woman from falling into the ravine on a runaway carriage, only to discover that she is Clara Clayton. She and Doc immediately become enamored with each other.At a festival dedicating the newly constructed clock tower, Buford, Nasty Jack, Cat R. Waul, Alameda Slim, and Team Rocket (Jessie, James, and Meowth) attempt to kill Doc, only to be thwarted by Marty, who threw a pie dish like a frisbee, causing the bullet to go into Doc's hat instead of his head. Marty, however, is goaded into a gun duel after Buford calls him "yellow". With Doc's original death averted, his name disappears from the tombstone in the photograph, but the date remains. Doc warns Marty that his name may end up on it if he chooses to meet up with Buford, Nasty Jack, Cat R. Waul, Alameda Slim, and Team Rocket (Jessie, James, and Meowth). Piglet replies "This is t-t-t-terrible." and Ash agrees. Still infatuated with Clara, the Doc expresses his desire to stay with her in 1885, but Marty talks him out of it. Doc decides to say goodbye to her and, when pressed, tells her that he's from the future. Thinking this an obvious lie, Clara angrily slaps him in rejection and starts to cry as Doc heads to the town saloon to get drunk. Marty, Pooh, Ash, Tennessee, and the others convince him to leave the saloon, but not before Buford, Nasty Jack, Cat R. Waul, Alameda Slim, and Team Rocket (Jessie, James, and Meowth) show up and insist that it's time for the showdown. Marty is forced to participate and defeats Buford by using a stove cover as a bullet-proof shield. Following the duel, Buford and Alameda Slim are arrested for having committed a robbery the previous day. Tigger blasts off Cat R. Waul into a big bag of mail and Pikachu uses thunder bolt to blasts off Team Rocket. Nasty Jack states now he can't trounce Marty and doesn't know what he's supposed to do. Marty suggests Nasty Jack that he could be the new sheriff of Hill Valley, and then Nasty Jack agrees and becomes Sheriff Jack. Clara, meanwhile, hears about how heartbroken Doc Brown was when she rejected him and sets off to find him.
Doc, Marty, Pooh, Ash, Tennessee, and their friends manage to hijack the locomotive and start to push the DeLorean; Marty, Pooh, Ash, Tennessee, and the others wait in the DeLorean while Doc remains on the train to add specially-created logs to the boiler that will overheat it and increase its speed. Clara catches up with the locomotive on horse and climbs aboard as Doc makes his way to the DeLorean. Seeing Clara in the cab, he is forced to return for her, and manages to fly off with her on the hoverboard just as the DeLorean reaches 88 miles per hour and transports Marty, Pooh, Ash, Tennessee, and their friends back to 1985 alone. The locomotive, which subsequently runs past the track, falls into the ravine and explodes. As planned in the parallel year 1985, Marty coasts safely across the ravine bridge, but he immediately encounters a modern-day diesel locomotive bearing down on him. Marty, Pooh, Ash, Tennessee, and the others escape, but the DeLorean is smashed to pieces. Marty, Pooh, Ash, Tennessee, and their friends pick Jennifer up at her house where he left her in Part II, and having learned his lesson back in 1885, refuses to take part in a drag race with Needles, who calls him 'chicken'. Marty shifts gears as if he's going to take the challenge, but as soon as Needles accelerates, he reverses to escape. As he watches Needles drive off, he discovers that he would have crashed into a Rolls-Royce. This causes him to avoid the automobile accident which resulted in the ruined future depicted in the previous film, as evidenced by the ripple effect erasing the fax Jennifer obtained from the future. Marty, Pooh, Ash, Tennessee, and the others take Jennifer to the site of the destroyed DeLorean, where he accepts that it is what Doc wanted. At that moment, however, a time machine built out of a locomotive appears and explodes out of nowhere, throwing Jennifer, Marty, Pooh, Ash, Tennessee, and their friends out of the way. After the strange locomotive stops in front of them, the door opens to reveal Doc, Clara and their two sons, who are named Jules and Verne, after Doc and Clara's favorite author, Jules Verne. (before appearing in Back to the Future: The Animated Series) named after the author Jules Verne. As Doc prepares to leave again, Marty asks if they plan to go to the future. Doc replies that they've already been there, as promised, Doc finally decides to take Pooh, Piglet, Tigger, Rabbit, Eeyore, Kanga, Roo, Lumpy, Darby, and Buster back to the Hundred Acre Wood and their time period and take Ash, Pikachu, Misty, Brock, Togepi, Tennesse Tuxedo, and Chumley back to their time, and the train lifts off from the ground and flies off into time, leading the viewers to think that Doc recently took the locomotive from 1885 to 2015 to get it fixed up and hover converted before returning to check on Marty. After dropping Pooh and the others off at their homes, Doc and his family leave for another time/ As the film ends, Genie appears saying "Wait a minute. We're not getting outta here, man! We're not getting outta here! Don't you understand it, man?! This is it. Game's over, man!" and then happily disappearing into the middle of the screen.
- Ash Ketchum, Misty, Brock, Pikachu, Togepi, Tennessee Tuxedo, Chumley, Nasty Jack, Cat R. Waul, Alameda Slim, and Team Rocket (Jessie, James, and Meowth) guest star in this film. Genie will make a brief cameo at the very end of the film. The main reason why Nasty Jack, Cat R. Waul, and Alameda Slim guest star in this film is because it takes place in the western Hill Valley.
- Jessie, James, and Meowth of Team Rocket will team up with Alameda Slim again in Littlefoot's Adventures of Home on the Range.
- This is Nasty Jack's second guest appearance (as he works for Buford "Mad Dog" Tannen): the first was Pooh's Adventures of An American Tail: Fievel Goes West, where he worked for Cat R. Waul.
- This is an NTSC film with NTSC bits from the Winnie the Pooh movies, the Pokemon movies, An American Tail: Fievel Goes West, and Home on the Range.
- Both Back To The Future Part III And American Tail: Fievel Goes West Are Executive Produced By Steven Spielberg, Frank Marshall, and Kathleen Kennedy, And Distribuited By Universal Pictures And Amblin Entertainment in The 90's.