The story begins exactly where Winnie the Pooh Goes Back to the Future left off. Marty McFly, "Doc" Brown, Jennifer Parker (now played by Elisabeth Shue), Winnie the Pooh, Piglet, Tigger, Rabbit, Eeyore, Kanga, Roo, Lumpy, Darby, Buster, Ash Ketchum, Misty, Brock, Pikachu, Togepi, Tennessee Tuxedo, and Chumley arrive at Marty's house to take them to 2015. After recovering from her initial shock, a consequence of parallel time travel, Jennifer begins asking many questions about her future. Doc tranquilizes Jennifer, who is not necessary for his plan, explaining that he brought her along only because she saw the time machine. After landing in Hill Valley, Marty, Doc, Pooh, Ash, Tennessee, and the others leave Jennifer in an alley, expecting her to remain unconscious while they attend to the crisis involving Marty's children. Doc explains that Martin McFly Jr., Marty and Jennifer's future son, is about to be approached by Griff Tannen, Biff's grandson, and his gang, who will offer him the chance to take part in a robbery. According to Doc, this event starts a chain reaction that leads to the ruin of the entire McFly family ("They've got to be ridiculous" comments Tennessee). Marty impersonates his future son and tells Griff he will not join the robbery; however, his self-control crumbles when his courage is called into question, and he is accused of being a "chicken". The resulting confrontation leads to a hoverboard chase that causes Griff and his thugs to damage the glass facade of the nearby courthouse. Griff and his gang are arrested and the planned robbery never occurs.
Before reuniting with Doc, Marty, Pooh, Ash, Tennessee, and the others notice a sports almanac displayed in a store window, which lists sports statistics from 1950 through to 2000. They buy it, intending to take the book back to 1985 and use the data within for financial gain. Doc discovers the almanac, and sternly tells Marty and the rest of the group that the purpose of inventing this time machine was for scientific investigation, not financial gain (especially dishonest), and pitches the almanac into a garbage can. Meanwhile, Jennifer, still tranquilized, is found by the police, who mistake her for her future self after thumbprint identification, and take her to her future home, waking her up just as they arrive. Confused, she hides in a closet, not seeing Marlene McFly, Marty's and Jennifer's daughter, letting George and Lorraine. She also witnesses the Marty of 2015 being fired from his job after his Japanese boss Mr. Fujitsu catches him "cooperating" in an illegal scheme (a sting operation) that his immediate boss and longtime friend, Douglas Needles, goads him into joining, again by taunting him that he is too "chicken" to try it. Travelling to the house, Doc leaves Marty with the DeLorean, finds Jennifer and sneaks her out of the house. Along the way, she encounters her older self, who has just arrived home, with the shock causing both women to pass out. Unable to carry her himself, Doc calls Marty for help, leaving the DeLorean unguarded.
While Doc and Marty rescue Jennifer, the original Biff (age 78), having overheard Doc and Marty talking about time travel and about the folly and hazards in using it to win at gambling, recovers the discarded sports almanac, steals the DeLorean and travels back in time. He returns the car just before Marty and Doc return to it to leave for their own time, stumbles away in pain and collapses (he has the same symptoms that Marty exhibited in Winnie the Pooh Goes Back to the Future when he was beginning to be "erased"). Bonus features on the DVD allude to the fact that Biff was killed by Lorraine in 1996. Upon arrival in 1985, Marty, Doc, Pooh, Ash, Tennessee, and the gang find that Hill Valley has become a dilapidated, crime-ridden slum lorded over by a middle-aged Biff, who is now immeasurably rich and powerful thanks to decades of successful sports betting with the help of Jessie, James, and Meowth of Team Rocket, the proceeds of which they invested in toxic waste dumps and to purchase the Hill Valley courthouse and convert it into a luxury hotel and casino. Biff has also married Marty's widowed mother, Lorraine, after secretly killing her husband George. Doc deduces that the Biff of 2015 must have given the almanac to his younger self sometime in the past. Marty, Pooh, Ash, Tennessee and the gang confront Biff and Team Rocket and find out that he received the almanac on, 1955, the date of the lightning storm that Marty, Pooh, Piglet, Tigger, Rabbit, and Eeyore used to get back to the future. Biff and Team Rocket then intend to kill Marty and the group (telling him that it's the same gun that he used to kill Marty's real dad George) as he now knows too much. Marty, Pooh, Ash, Tennessee, and the others again are saved by Doc when Doc knocks Biff out with the DeLorean's gull-wing door, but Jessie, James, and Meowth jump onto it to team up with the young Biff in 1955.
Marty, Doc, Pooh, Ash, Tennessee, and the gang travel back to 1955 to prevent Biff from getting the almanac. Marty, Pooh, Ash, and Tennessee go through a long and complicated series of events involving his multiple attempts to recover the almanac while making sure that they do not undo all the help they rendered in the previous film to Marty's parents (this includes almost running to their other selves from the first film while the latter is at the prom with Marty's mother and when he plays "Johnny B. Goode" with Pooh and the others dancing to the song). He eventually manages to steal the book from the 1955 Biff with the help of Doc in the flying DeLorean (with Tigger blasting off Team Rocket after the 1955 Biff is defeated), and burns it, restoring history to its proper course. As Doc fights the controls (and accidentally turns on the time circuits which were malfunctioning with the Destination Time readout showing the destination as January 1, 1885.) while attempting to land the DeLorean during the storm to pick Marty, Pooh, Ash, Tennessee, and the gang up, the car is struck by lightning, causing it to disappear, the flux capacitor having been triggered by the lightning. A few minutes later, a Western Union delivery man appears with a letter, which he explains was sent seventy years ago with the explicit instructions that it be delivered to Marty "at this exact location, at this exact minute, November 12, 1955". Marty, Pooh, Ash, Tennessee, and the gang open the letter, which is from Doc, explaining that he is now living happily in 1885. Knowing he has only one source of help, Marty and company run to the clock tower to find the Doc of 1955, just as lightning strikes to send the previous film's Marty, Pooh, and the gang back to the future. The shock of suddenly seeing the new Marty, Pooh, and the gang (with Ash, Tennessee, and the others with them this time) whom (he thinks) he has just sent back to 1985. Doc exclaims, "Great Scott!" and faints. The film ends as Marty and the others bend over Doc, trying to revive him. The film ends with the words "To be concluded in Winnie the Pooh Goes Back to the Future Part III" on the screen.
- Ash Ketchum, Misty, Brock, Pikachu, Togepi, Tennessee Tuxedo, Chumley, and Team Rocket (Jessie, James, and Meowth) guest star in this film.
- Jessie, James, and Meowth of Team Rocket will work for both the alternate 1985 and 1955 Biff Tannen in this film.
- This is an NTSC film with NTSC bits from the Winnie the Pooh movies and the Pokemon movies.