After managing to calm down Buu's rage by dealing with the thugs himself, Mr. Satan discovers that the dog is barely alive, with Buu managing to heal him just in time. As Buu, Mr. Satan, and the dog start becoming closer, Mr. Satan decides to stop taking advantage of Buu's innocence and become his earnest friend. However, the thugs from earlier show up and shoot Mr. Satan, once again causing Buu to be overcome with anger. After healing Mr. Satan, Buu instructs him and the dog to get away from him, as the evil in his body escapes and transforms into a tall, grey, emaciated version of Majin Buu.

Buu attempts to fight against the Evil Buu, but out that finds he is much weaker, as most of his power had been transferred over to his evil side. As such, Evil Buu manages to reflect Buu's candy attack back at him, turning him into chocolate before eating him and gaining his power, giving him a more complete form. Sensing the energy of Piccolo and the others, Evil Buu arrives at Kami's Palace, demanding to fight against Gotenks. Piccolo attempts to stall for time by telling Evil Buu to wait until all earthlings are killed, instructing Krillin to bring Goten and Trunks to the Hyperbolic Time Chamber to make use of what little time they have.

Piccolo's hopes of being able to buy some time are dashed when Evil Buu unleashes a powerful homing attack which targets and kills every human on the earth, with the exception of Mr. Satan, Tien, and Chiaotzu. Piccolo, along with Videl, manages to convince Evil Buu to wait for an hour so that Goten and Trunks can train. Meanwhile, Gohan, tired of waiting any longer for Old Kai's power-up, discovers that he has indeed managed to increase his power and agrees to wait for the power-up to be completed. Becoming further angered when Evil Buu kills an impatient Chichi, Goten barely holds in his anger and joins Trunks in the Hyperbolic Time Chamber. With Evil Buu growing impatient after only thirty minutes, Piccolo tries to buy as much time as possible as he slowly leads Evil Buu to the chamber, believing that even if Goten and Trunks fail, they can destroy the chamber's entrance and trap him there.

Piccolo continues to lead Evil Buu to the Time chamber, when Goten and Trunks train hard to avenge the loved ones that they have lost. After rerouting Buu through Kami's palace, due to Buu being extremely unhappy and throwing tantrums every now and then, Piccolo takes Buu to the Time chamber, and Gotenks fights Buu after a warm-up round and playing around.

Super Buu and Gotenks begin to fight, and Gotenks decides to use some of his new special moves. The problem is that these moves, while flashy, are ineffective against Buu, not to mention they have ridiculous names, like the "Screaming Angry Wombat". After it is clear that these moves have no effect, Gotenks talks strategy with Piccolo. He then creates a ring of energy, the "Galactic Doughnut" and uses it to trap Buu. After a brief struggle, Buu is able to break the ring. The two then do a bit of real fighting. Gotenks decides to use another one of his special moves, called the Super Ghost Kamikaze Attack. He spits out a ghost of himself, and plans to use it against Buu. Gotenks creates ten ghosts that detonate with explosive force when they are touched. He sends all but one at Super Buu, and they reduce him to a deformed puddle of his former self. Gotenks sends the final one down Buu's mouth, blowing him into tiny pieces. Gotenks and Piccolo destroy all of the pieces, but the smoke coming from the pieces gathers above their heads and reforms Super Buu. To play up the drama of the situation, Gotenks acts like he's out of ideas, and Buu begins beating up the fused Saiyan. Thinking that Gotenks cannot stop Buu, Piccolo destroys the door to the outside world, which traps the three of them in the Chamber for all eternity.

Hysterically upset at the prospect of being trapped in the Hyperbolic Time Chamber forever, with nothing to destroy and no candy to eat, Super Buu starts to scream. To everyone's surprise including his own, his screams become so powerful that they create a hole in the barrier between the dimensions of the chamber and Earth. Buu changes shape in order to fit through it, and the hole closes, leaving Piccolo and Gotenks trapped. Back on The Lookout, Buu is hungry and excited at the prospect of turning more people into food, and so he turns everyone on the lookout into chocolate. Piccolo and Gotenks have been attempting to scream loud enough to create an inter-dimensional hole like Buu did, but they have no success. Gotenks decides to play his trump card, transforming into a Super Saiyan 3. In this state, he has the power necessary to create a hole for him and Piccolo to jump through. Upon their return to the lookout, Buu tells Gotenks that he ate all of his friends, and enraged, Gotenks promises Buu that he will pay.

Gotenks and Super Buu begin to fight, and the collateral damage from the battle begins to destroy The Lookout. Buu slams Gotenks down through The Lookout itself. Down on earth, Gotenks tries another Super Ghost Kamikaze attack, but it once again fails. Buu lands a powerful hit on Gotenks that sends him flying back into The Lookout. Buu then folds himself into a ball, and begins repeatedly shooting himself through The Lookout until all that's left is rubble floating in the air. While still in a ball, Gotenks is able to trap him in a little sphere. He and Piccolo then play some volleyball with Buu, and Gotenks spikes him down to earth. Just when it seems like Buu is dead, a powerful blast of energy comes from the crater. With Buu once again ready to fight, Gotenks only has a few minutes until he separates.

Gotenks and Buu continue their fight. Gotenks seems to be wearing Buu down, and he now has the upper hand in the fight. Just as he's about to hit Buu with his final move, Gotenks unexpectedly returns straight to his normal state from his Super Saiyan 3 form. The power was too high for him to sustain. Buu begins beating up Gotenks, who is now no match for him. Gohan has finally finished his training, and is ready to return to earth. After saying goodbye to Goku for what they both believe will be the last time, Kibito takes him back, and Gohan asks him to change his clothes. He's now wearing clothes just like Goku and arrives just in time, because Gotenks has separated.

Gohan arrives at the scene, and everyone is shocked at how much power he has. After Gohan expertly pounds him to a pulp, Buu heals himself and steps up the intensity, but Gohan still has the upper hand. He is easily picking Buu apart. Realizing that he's totally outmatched, Buu decides to self-destruct, hoping to take Gohan with him. Gohan escapes before Buu explodes, and he takes the others with him out of the blast radius. Afterwards, there is no sign of Buu, but Gohan knows that he's still around. They suddenly detect Dende's energy signal, and they go to find him. On the way, they pick up Hercule Satan and the dog, Bee. Dende explains that as Buu was escaping through the interdimensional hole, Mr. Popo threw him from the lookout, because without Dende, there would be no Dragon Balls to grant the wishes they intend to use to reverse all the damage. Buu tracks them down, but instead of having a rematch with Gohan, he calls out Goten and Trunks.

Unknown to the others, Buu secretly separates two chunks from his back, and the two pink blobs creep around behind the others. As soon as Goten and Trunks fuse, one of the blobs encases Gotenks. Piccolo, too, has been covered by a pink blob. Buu calls each of the blobs back to him, which merge with him, changing his appearance and giving him access to all of Piccolo's and Gokenks' memories, abilities and power. The new and improved Super Buu then fights Gohan, and it's clear that Buu has the advantage. Gohan is unable to keep up with Buu's new speed and strength. Buu taunts Gohan by telling him what his three friends that were absorbed think of him.

Gohan is no match for the new Super Buu. Buu now possesses new skills, such as the Super Ghost Kamikaze Attack and the Special Beam Cannon, each of which he uses on Gohan. He is about to finish Gohan, when Bee comes running up. Hercule tries to save Bee, but is only several times stronger than the average human - nothing compared to Buu. Buu is about to blast each of them when Gohan saves them. Buu then uses Gotenks' Galactic Doughnut trick on Gohan, and aims a Kamehameha wave at him, but Gohan is able to summon enough strength to break free and move out of the way in time. Meanwhile, in Other World, King Yemma decides to send Vegeta back to earth to help in the fight against Majin Buu. On the world of the Kais, Old Kai decides to give his life to Goku so he can return to Earth and fight Buu. The now deceased Old Kai gives Goku his earrings. He explains to Goku that if he and another person each wear one, they will fuse together.

Old Kai tells Supreme Kai and Kibito to try a fusion with their earrings, but only after they fuse together does he reveal that it is a permanent fusion. Dende heals Gohan's injuries, so to prevent this from happening again, Buu creates a giant energy ball and aims it at Dende. Just before it hits, it is deflected by Tien's Tri-Beam attack, who has decided to help, even though he is terribly outclassed. Buu tries again, but Goku suddenly appears and sends a disk of energy at the monster. It cuts off his legs and part of his head. His legs deal Tien a crushing kick which completely incapacitates him and then they return to Buu. Desperate to stop Majin Buu, Goku throws Gohan the other earring, but his aim is off and the earring is lost in the rubble. Goku goes Super Saiyan 3 in an attempt to hold Buu off while Gohan searches for the earring. Inside Super Buu, Gotenks' fusion wears off, splitting back into Trunks and Goten, causing Buu to lose well over a third of his power and his appearance to change. Realizing what's happened, Goku declares he can now defeat Majin Buu without fusing with Gohan and prepares to fight. Knowing he needs a massive power increase, Buu causes the part of his head that was cut off earlier to suddenly engulf Gohan, just like Piccolo and Gotenks. He reabsorbs the blob containing Gohan, and is now even more powerful than he was with Gotenks absorbed. Now back in control, Buu toys with Goku, telling him he has some time to find someone to fuse with. He considers fusions with Dende and Hercule, but neither of them are appealing possibilities. He suddenly senses that Vegeta has returned, and uses Instant Transmission to teleport to his location. While Buu is distracted, Dende heals Tien. After Goku finds Vegeta, Goku tries to convince him to fuse, but Vegeta is angry at Goku because he knows Goku was holding back his Super Saiyan 3 transformation when they fought. With Vegeta refusing to cooperate, they are forced to take on Buu as individuals, but are clearly outclassed. Goku tells Vegeta that Buu absorbed Trunks and killed Bulma and asks him to put their differences aside to save their people. Vegeta finally agrees, and only when he puts the earring on does Goku mention that the fusion is permanent. The two last surviving Saiyans fuse and a new being is created.

The new being names himself Vegito, and begins to fight Buu. He clearly is far superior to even the new Super Buu. In Other World, Bulma, Videl, Chi Chi, and Dabura are looking for Gohan, whom they mostly believe to be dead. When Dabura arrived at the Check-in Station, he resisted the guards attempts to subdue his aggressive behavior, and knowing Dabura would enjoy being sent to hell, King Yemma turned him good. Back on earth, Dende and Hercule arrive at the battle scene, just as Buu has decided to destroy the earth. He creates a massive ball of energy, and throws it towards the earth. Vegito easily catches it, and deflects it back out into space. Buu claims that he has yet to fight at his full power. Vegito says the same, and powers up to a Super Saiyan. Now calling himself Super Vegito, he continues to thrash Super Buu. Buu tries to hide himself with his own steam to gain an advantage, but Vegito continues to batter him. On the Grand Kai's planet, Krillin and Yamcha are training with King Kai. Back on earth, Buu is starting to become desperate. He liquifies himself, and shoots down Vegito's mouth, entering his body and turning him into what looks like a super-muscular version of himself. While inside Vegito, Buu takes control of his body and boasts that he will use him to destroy him from the inside, but Vegito uses his energy to isolate all of Buu into one spot and pound him. Buu moves around but Vegito simply continues to pound him. Buu is forced to exit Vegito's body. Realizing he doesn't know how he can save himself, Super Majin Buu begins to freak out, and the immense amount of energy he releases into his surroundings threatens to tear apart the universe itself. Realizing this, Vegito tries to stop him, but Buu has put up a shield around himself. After a long struggle, Vegito breaks through the shield and stops Buu.

Vegito and Buu continue to fight, but Vegito is still far more powerful than his opponent. He repeatedly dominates Buu, which makes Buu angrier and angrier. Vegito is just toying with him. Buu hatches a plan, and calls Vegito out. Vegito comes closer, and Buu turns him into candy. As Buu celebrates his apparent victory, the Vegito candy unexpectedly begins to attack Buu. It turns out that Vegito is somehow still in full control of his new, candy body, and that he is just as powerful as he was before, and can even still talk! (Albeit in a higher pitch). The candy Vegito is just as fast as Super Vegito, and due to its tiny size, is impossible for Buu to hit. Infuriated at being toyed with by a piece of candy, Buu changes it back into Vegito, who then continues to beat him up. Vegito literally starts tearing Buu apart. He gives Buu until the count of ten until he destroys him, and during this countdown, Buu notices a part of himself that Vegito tore off down on the ground. This part rises up behind Vegito, and before Vegito reaches ten, he is engulfed by the pink blob. Buu calls the blob back to him and absorbs it.

After absorbing Vegito, Buu notices that he has not taken on any of his characteristics. He guesses this is because he hasn't digested Vegito yet. Inside Buu, Vegito still exists intact, and separate from Buu. It turns out that Vegito had planned this, putting up a barrier during the absorption, and letting himself be shrunk by Buu's magic absorption process, but not incorporated into his being. Once he dispels the barrier, Vegito unexpectedly splits back into Goku and Vegeta. Taking advantage of this unexpected event, Vegeta crushes his fusion earring, not wanting to give up his independence from Goku by permanently fusing with him. He cites that once they free their absorbed friends, Buu will lose most of his power and they won't need to be fused to defeat him. Goku and Vegeta cut down the cocoons of Gohan, Goten, Trunks, and Piccolo, and as they do, Super Buu regresses to his normal form. Dende and Hercule continue to follow Buu. Back inside Majin Buu, Goku and Vegeta also find the fat Majin Buu. They read his thoughts to find out what happened to him. Suddenly, a thought form of Super Buu himself appears. The two join forces to defeat it, but once they do, another one appears. They realize that this is a battle they cannot win. Buu finally decides that he's had enough, and he tries to absorb Goku and Vegeta.

Goku saves Vegeta from being absorbed. As Vegeta recovers, Goku continues to fight the thought form of Super Buu. Goku is rapidly losing energy, and just as Super Buu is about to defeat Goku, Vegeta cuts down the pod containing the fat Majin Buu. This causes Super Buu to go mad, as without the fat Majin Buu absorbed, Super Buu cannot exist. As Super Buu's insides begin to change, Goku and Vegeta realize they must leave, and so they grab the pods containing Gohan, Goten, Piccolo and Trunks and try to find a way out. On their way through his body, they notice one of the tunnels that leads to one of the holes in Buu's skin where the steam escapes. They are able to fly out through here, and when they emerge on the other side, all six of them regain their normal size. As Goku and Vegeta set the pods down, they observe Super Buu changing into a different being. He first transforms into a hulking form, and then shrinks into a childlike version of himself.

Supreme Kai explains to Old Kai that there were once one five Supreme Kais. He was one of the four that each ruled over a quadrant of the universe, and the fifth was their leader. He says that this latest, childlike version (Kid Buu), is the original, true Majin Buu, and by far the most powerful of them all. Supreme North and West Kai perished against him. Supreme South Kai was absorbed, changing the original Majin Buu into the hulking form that was seen briefly in the previous episode. The leader, Dai Kaio, was then absorbed by that form, but this absorption changed Buu into the fat, happy Buu that came out of the ball. This absorption of the Kais actually weakened Buu, making him less focused and less destructive. Back on earth, Kid Buu creates a powerful ball of energy and throws it at the earth, intending to destroy it. Goku and Vegeta deflect it. In retaliation, Kid Buu then a creates a ball ten times more powerful than the previous one and throws it. Knowing that they currently do not have enough strength left to stop it, Goku and Vegeta try to grab everyone and teleport away, but are only able to grab Dende, Hercule, and Bee. As the Earth is about to be destroyed, Supreme Kai appears and instantly transmits Goku, Vegeta, Dende, Hercule, and Bee to the world of the Kais.

Kid Buu is blasted apart by the explosion, but he reforms after the destruction of the Earth, and goes on a rampage throughout the galaxy. He goes from planet to planet, looking for Goku and Vegeta, and then destroys each planet when he doesn't find them. He goes to the Grand Kai's planet, and starts to toy with everyone there. When he becomes bored, he creates an energy ball, intending to destroy the Grand Kai's planet. Supreme Kai offers Goku and Vegeta his fusion earrings, but they both refuse them. They raise their power levels so Buu will know where to find them. Buu abandons his attempt to destroy the Grand Kai's planet and teleports to the world of the Kais. The Supreme Kai transports himself, Dende, and Old Kai to a distant planet so they will be out of Goku and Vegeta's way, along with a crystal ball that allows them to watch the battle. Unfortunately, they forget to take Hercule and Bee along. Goku and Vegeta play rock, paper, scissors to decide who will fight first, and Goku wins. He powers up to Super Saiyan 2, and starts beating up Buu. Goku blasts him apart, but he reforms. Buu creates another massive energy ball and throws it down at the planet. Goku is able to deflect it, but Buu guides the ball back around and into the planet. Powerful shock waves rock the entire planet, disfiguring its shape and leaving the surface ragged and uneven. Goku decides to power up to Super Saiyan 3.

Goku and Kid Buu continue to fight, each taking powerful blows from each other. Kid Buu folds himself into a ball again, and hits Goku hard. Goku puts all of his energy into a massive Kamehameha, but Buu just reforms afterward. Goku returns to his normal state, collapsing from exhaustion. Vegeta then steps in, but that finds he is no match for Buu. Buu cleans his clock, and just as he's about to deal Vegeta the finishing blow, Goku pushes him out of the way. He then powers back up to Super Saiyan 3 and continues their furious fight. Vegeta reminisces about all of the fights he and Goku were in. He finally admits to himself that Goku is better.

Goku continues to fight Buu, and he seems to have the upper hand. He deals a lot of damage to Buu, but as the fight goes on, his hits become weaker and weaker until they have virtually no effect at all. He tells Vegeta that it's his turn, but Vegeta declines, deciding that he is no match for Buu. He tells Goku that Buu is too powerful for him and that Goku stands a much better chance of destroying him. Goku is shocked and unsettled by this admission, telling Vegeta that he deliberately let the fight drag on so that Vegeta could have a turn, and that now he is exhausted. Vegeta is horrified by this, because now they cannot stop Buu. Goku unsuccessfully attempts to reassure Vegeta, telling him that he needs one uninterrupted minute to power up enough to destroy Buu. Despite the fact that Vegeta recognizes that he will need a miracle to survive a minute against Buu now, he reluctantly steps in while Goku is powering up, even though Goku tells him that if he is destroyed when he is already dead, Vegeta will no longer exist in any form. Buu thrashes Vegeta, but every time he gets knocked down, Vegeta gets up, ready for more. Buu stretches out his arm, wraps it around Vegeta's neck, and begins choking him for fun. It's been more than one minute, but Goku still hasn't generated the power he needs.

Fat Majin Buu enters the fight, saving Vegeta from death. However, he is no match for Kid Buu, who begins to severely beat him. Hercule tries to help Fat Buu, but is ineffective. Vegeta suddenly comes up with a plan. He communicates with Dende, telling him to go to New Namek and gather the Dragon Balls. The Supreme Kai and Old Kai take Dende there, and the Namekians are waiting with the seven balls. Porunga is summoned, and Vegeta tells Dende his two wishes: bring back the earth and restore it to its undamaged state, and bring back all of the non-evil people that died since the morning of the World Martial Arts Tournament. These wishes are granted, and even Vegeta himself comes back to life, proving that he is no longer evil. He finally reveals the main part of his plan to destroy Buu: the Spirit Bomb.

The people of earth come back to life, including the Z Fighters and their friends. Goku gets into position to create the Spirit Bomb, and with the help of King Kai, Vegeta speaks to the entire population of earth. He tells them what's going on, and that to defeat Buu, they need to raise their hands up and offer their energy. Only Goku and Vegeta's family and friends comply. No one else is willing to listen to a mysterious voice from the sky. Vegeta repeatedly pleads with the earthlings, but to no avail. While this is going on, Fat Buu is buying them time by fighting Kid Buu, but it's not going well. Goku hasn't gathered nearly enough energy to destroy Buu.

Vegeta continues to plead with the people of earth, but no one will listen to him. Fat Buu has finally lost all of his energy, so Vegeta is forced to fight Kid Buu. He is no match for him, and gets severely beaten. Now Goku asks the earthlings to raise up their arms and donate some of their energy, and small pockets of people who recognize his voice or just like the sound of it do so, but the vast majority remain uninterested. Piccolo, Gohan, Goten, and Trunks spread out into the city, hoping to convince people to raise their arms. Hercule has finally had enough, and he speaks to the people of earth. When they hear the familiar voice of the "World Champion," all of the people of earth raise their arms and offer their energy. The Spirit Bomb is finally ready.

Goku is ready to throw the Spirit Bomb, but Vegeta is in the way, and, despite Vegeta's pleas otherwise, he refuses to take out Vegeta along with Buu. Suddenly, Fat Buu gets up and holds Kid Buu down long enough for Hercule to pull Vegeta to safety. Kid Buu kick Fat Buu aside, and Goku throws the Spirit Bomb. It hits Kid Buu, but he starts pushing it back. Goku uses all of the remaining energy he has left trying to push it back into Kid Buu, but he is too powerful. After a brief panic, Vegeta suddenly remembers that they still have a third wish with Porunga. He instructs Dende to wish for Goku's power level to be restored to its normal, healthy level. The wish is granted, and upon turning into a Super Saiyan, Goku is easily able to force the Spirit Bomb back at Kid Buu. As he does so, he silently wishes that Buu had been a better person, and hopes to fight him as a different person, some day in the future. The Spirit Bomb hits with full force, finally destroying the evil, childlike Majin Buu permanently. After billions of years of destruction, he has finally been brought to justice.

Ten years have passed, and much has changed. Gohan has become a scholar, and Trunks and Goten are in their late teens. Goku is training with Goten when Bulma and Vegeta, who have a new daughter, Bulla, show up after not seeing him in five years. Goku says that he and Goten will be entering the World Martial Arts Tournament, so Vegeta says that he and Trunks will do the same. The day of the tournament comes, and old friends catch up. Everyone has arrived to watch. Gohan, who is now married to Videl, has decided not to enter, but his daughter, Pan, will fight. Since there is no junior division this time, she will be fighting with the adults. Hercule and Buu will also be fighting. However, Goku says that there is someone who is 100% human that can threaten to beat him and Vegeta. The seeding draw for the tournament begins, and Goku asks Majin Buu to use his magic to rig it so that he faces the powerful mystery fighter he had talked about. In the first match, Pan faces Wild Tiger, and the four-year-old easily dispatches him. Next up is Goku against a ten-year-old boy named Uub. Uub is the reincarnation of the evil Kid Majin Buu. King Yemma apparently heard Goku's wish right before the evil Buu was destroyed, and he reincarnated him as a good person named Uub. Uub is apprehensive, so to bait him into fighting, Goku eventually resorts to taunting the young boy. After a particularly nasty insult and a kick to the face, Uub has snapped, and is now ready to fight.

Goku and Uub begin to fight, and it is clear that Uub does not know much about fighting. But as the match goes on, he learns more and more, and more and more of his hidden power is released until he is able to go toe to toe with Goku in his base state (without Goku powering up). When Goku does power up slightly (in his normal state) Uub nearly falls out of the ring, but Goku saves him from hitting the ground. He realizes that Uub doesn't even know how to fly, so Goku decides to train him. Despite his friends and family pleading with Goku to stay, he flies away with Uub on his back. Goku decides to train Uub to defend the Earth when he's gone. He hopes one day, when Uub's training is complete, to have a real all-out match with him to test their power. Goku and Uub fly off into the distance with whoops of joy.