The movie starts with Michael Jackson singing his hit song "Man in the Mirror." After that song is over a montage starts of Michael as a kid and works it's way up to present day. After the montage is over, the music video for "Bad" is being remade by various child performers with the name "Badder." After the video is over, the young Michael is walking out of the builiding he is in. Outside, a claymation tourbus pulls up to the builiding. A large cloud of mist is seen on both sides of the builiding and when young Michael walks through, he turns back into present day Michael. The people in the tourbus spots him and begin to chase him.
After awhile of chasing, Michael accidently runs into an area where they are filming a movie. The director yells at him and the two actors decide to chase him as well. Michael manages to hide in a wardrobe room and sneak out dressed as a bunny, riding away on a bicycle. The paparazzi soon realize what happened and begin to chase Michael again. Michael's bike shifts into a Harley-Davidson motorcycle and the music video for "Speed Demon" begins. After Michael is sure he has lost his fans he stops in the desert and take off his bunny suit and sets in on a rock. He starts to walk away when something taps him on the shoulder. The bunny suit has come alive and it seems to challenge Michael to a dance contest. After a little dancing, a police officer taps Michael on the shoulder and gives him a ticket, Michael also noticed that the bunny has vanished. Michael gets on his motercycle and just before he rides away, the mountain in front of him takes shape of the bunny and winks at him. Michael smiles back and drives away. Then the music video for "Leave Me Alone" starts.
Once the "Leave Me Alone" segment is over, the quite rare, very long "Smooth Criminal" video begins. We see a full moon and three little kids on a rooftop looking at a builiding. Sean (Sean Lennon), Katie (Kellie Parker), and Zeke (Brandon Quintin Adams). Michael steps out of the builiding they are looking at and looks up at the sky. Then we see someone cracking a peanut in his hands, and Michael looks over to them and dodges quickly as henchmen start shooting at him. The two boys in fright, run away, and Katie stays behind frozen. She starts shouting Michael's name and then we go to a flashback.
We see Katie, Sean, and Zeke playing in a field with a soccer ball and along with Katie's dog Skipper. Someone kicks the ball and Skipper runs over, picks it up with his mouth and runs into the woods. Michael goes to look for him and Katie comes along with him. They call out to Skipper who is no where to be seen. They soon find a section of the woods covered with nothing but spiderwebs and locate a secret tunnel inside a rock. They both follow it trying to be as quiet as possible. When they see people, they stop on a staircase and look to see what they are talking about. They overhear someone who plans to get every child in the world hooked on drugs. The villan identifies himself as Franky LiDeo (Joe Pesci). Named Mr. Big for short. Katie sees a spider about to crawl on her arm and starts to scream. Mr. Big sees them and sends his gunmen after them.
We go back to the building where Michael is trying to dodge the bullets being shot at him. After the gunmen stop shooting, we see that Michael has gotten away and is running for his life. Katie notices this and runs off the building to find her two friends. After a while of running, Michael is cornered in a dead end and Mr. Big and his guards go to kill him when Michael's lucky star goes by. His lucky star can make him do anything or turn into anything. Michael turns himself into a super fast car and speeds past his enemies, escaping.
We now see Katie entering an abandoned club, and Sean and Zeke are both hiding there and greet her. They all claim Michael told them to meet him there earlier. They leave the club to make sure they are at the right place, and they run behind a fence when they hear someone coming. Katie looks over and sees Michael transforming back into human form. She is in shock and after she gets better, they all look up and see him entering the club. A burst of white light flashes and Michael enters. It turns out to be a lively, crowded, gangster-infested 1930s American nightclub. Michael is surprised by this, and everyone in there is surprised to see him. Michael feels it is his job to entertain them, and so, he performs his hit song, "Smooth Criminal". Despite the fact that the song "Smooth Criminal" is four minutes and seventeen seconds, this scene is dragged out to be about ten minutes long. Towards the end of Michael's exciting performance, Katie is kidnapped by Mr. Big while Sean and Zeke are still hiding behind the fence. Michael runs out to find what happened and they all go looking for her.
They find Mr. Big's lair and enter trying to be as quiet as possible. Sean and Zeke stop while Michael goes ahead. Then a metal door closes behind him, separating them. Michael runs to the center of the room and the boys go to the roof. A spotlight hits Michael and follows him until he is cornered. Then all the gunmen come out and point their guns at him, and two guards go infront of him. We hear Katie screaming as she is coming up an elevator. Mr. Big has a hold of her and is hitting her several times. Michael tries to go to her but the guards hold him back. Mr. Big reveals that he "just wants to get everybod high, " and is about to inject Katie with a drug when she scratches his face and runs to Michael. At the same time, the guard takes the back of his gun, hits Michael once in the stomach and once in the face. Giving him a concussion. Mr. Big catches Katie and pulls her back, turns Michael over and kicks him once in the chest. Michael is on the floor in pain and Katie tries to crawl away but is stoppped, Mr. Big orders the men to kill her first. Michael screams at him to leave her alone when his lucky star flies by and he transforms into a giant robot! Mr. Big manages to escape after Michael has killed all of the guards. Including the guard that was keeping Sean and Zeke on the roof. Michael then turns himself into a space ship and kills Mr. Big when he tries to kill him with a cannon. The kids are confused as to why they were left behind and say goodbye to Michael as he flies away thinking they would never see him again.
We then see the kids sitting on a bench in the street saying how much they miss him. Katie gets up to sit in a corner and she says to herself that she wishes he would come back. Just then we see mist and Michael appears out of nowhere. They all see him and run to him in happiness. He tells them to follow him and he leads them to the club, informing them that there is a surprise in store. Once again, a burst of white light flashes when they enter. It is at this point, when the quite rare, very long "Smooth Criminal" video ends, and the "Come Together" sequence begins. This is where the kids get Skipper back, and Michael performs his closing song "Come Together."