In the Yu-Gi-Oh! GX anime, the "Super Polymerization" card is a symbol of the absolute power and control. Yubel, the spirit of Jaden Yuki's favorite card in childhood, orchestrated this card's creation so she could fuse all 12 dimensions together and rule over them with Jaden at its side. This card is created through the collection of negative emotions (i.e. anger, hatred, doubt, anguish, and sadness) into a single form. This can be achieved by sacrificing a small amount of individuals who personify negativity or by sacrificing numerous individuals. According to Yubel, this card is the mightest card in the Duel Monsters and a symbol of the Supreme King.
- In episode 135, Brron, Mad King of Dark World revealed during his Duel against Jaden Yuki that he is going to complete this card with the help of "Wicked Canon". Brron planned to make Jaden suffer and fight with his own friends in order to create negative emotions on both sides. By achieving this, enough negative energy would be created for Brron could sacrifice Jaden's friends to complete this card. The first of Jaden's friends to be sacrificed was Chazz Princeton, who carried the emotion of anger. In the next episode, Tyranno Hassleberry (hatred), Atticus Rhodes (anguish) and Alexis Rhodes (sadness) were sacrificed when Jaden tried to play defensively and Brron turned this plan against him by using "Dark Tournament" to force Jaden's monsters to attack. As his henchmen were busying trying to capture Syrus Truesdale (who represented doubt), Brron believed that he won't need the fifth sacrifice and tried to use "Wicked Canon" to activate this card. It doesn't work and Brron realizes that he would need the fifth sacrifice in order to complete this card. Brron abandoned the plan on completing this card and instead went for an alternative strategy. After Jaden defeated Brron and Jaden's remaining friends abandon him for his actions, this card landed in front of him. In his mind, he was holding the card as pictures of his friends in the mirrors disappeared one after another. The spirit of the Supreme King then appeared in his mind and convinced him that he must defeat evil by becoming evil and rule with power in that cruel world of deceit. The Supreme King told him that the required power is this card, which Jaden must complete by defeating and sacrificing the opposing spirits. At that moment, the King took control over Jaden.
- In episode 138, this card was mentioned by Kozaky, the Supreme King's researcher on it. He was referring to it as "the ultimate card". He stated that the Supreme King had defeated countless Duelists in order to complete "the ultimate card", starting at the Colosseum of Death, part of his castle, where he had achieved "the complete victory".
- In episode 139, Jim Crocodile Cook used the power of the Eye of Orichalcum to get him and Axel Brodie into Jaden's mind while Jim was Dueling the Supreme King. Jaden constantly asked himself what he had done wrong. After several flashbacks of his life-or-death Duels, he questioned what he had been missing and what a Duelist should carry inside himself. The spirit of the Supreme King appeared once again and told him he needed power. By carrying regret for souls he had lost, Jaden should turn it into power. This card then appeared in Jaden's hand where it was shown to be nearly completed. As Jim tried to confront him, the power of the Eye stopped and returned Jim and Axel to the Duel.
- In episode 140, the Supreme King uses this card during his Duel against Jim (this revealed that this card was completed prior to the Duel). He uses this card to discard "Fake Hero" and fuse "Evil Hero Infernal Gainer" with Jim's "Gaia Plate the Earth Giant" in order to Fusion Summon "Dark Gaia".
- In episode 143, the Supreme King uses this card during his Duel against Axel. When "Volcanic Doomfire" attacks "Evil Hero Malicious Edge", the Supreme King activates this card to discard "Vicious Claw" and fuse "Malicious Edge" with Axel's Evil Token in order to Fusion Summon "Evil Hero Malicious Fiend". A replay occurs, but due to "Malicious Fiend's" effect, "Volcanic Doomfire" is forced to attack it. "Malicious Fiend" then destroys "Volcanic Doomfire", but Axel banishes "Volcanic Counter" from his Graveyard via its own effect in order to make the Supreme King take the same amount of Battle Damage he takes, ending the Duel in a Draw.
- In episode 144, this card can be seen when Aster Phoenix checks Jaden's deck and takes out this card. Aster questioned Zane Truesdale why Jaden would have this card as it wasn't in his Deck before.
- This card is also shown in a series of flashbacks Jaden has when he sees the memories of the Supreme King within his nightmare.
- In episode 151, this card is seen in a series of flashbacks Jaden has when the dark memories of the Supreme King try to haunt him again. This time Jaden declares he won't run or lose his way as the pain, sadness, and hate that everyone felt is within him and he will fight it all the way. This is enough to conquer his fear of performing a Fusion Summon.
- In episode 152, Jaden uses this card during his Duel against Jesse Anderson while the latter was possessed by Yubel. As he drew the card, he called it "the card of darkness" which led him through hell. He remembered the people and spirits who died because of him, as the one he lost. Promising himself to protect what's most important to him till the end, he activates this card to discard "Contact Out" and fuse his "Elemental Hero Neos" with Jesse's "Rainbow Dark Dragon" in order to Fusion Summon "Rainbow Neos". This action turns "Rainbow Dark Dragon" back into "Rainbow Dragon" and frees Jesse's soul, which causes Jesse's soul to go back into his body and forces Yubel to exit his body. However, Yubel then activates "Last Trick" to add this card from Jaden's Graveyard to her hand. She then reveals that making Jaden into the Supreme King was so he would create "Super Polymerization" for her, and that possessing Jesse and dueling Jaden was all a ploy to take it from him. Yubel then activates "Thousand Buster" to pay 1000 Life Points, destroy all Attack Position monsters that have 1000 or less ATK, destroy all Defense Position monsters that have 1000 or less DEF, and inflict 1000 damage to both players, which ends the Duel in a Draw. Once that was done, Yubel flew off with this card now in her possession.
- This card also appears in Jaden's thoughts when he wonders if there's way to free Jesse's soul from "Rainbow Dark Dragon". Upon remembering this card, Jaden realizes that he will need to use it in order to free Jesse.
- In episode 153, Yubel uses this card during her Duel against Jaden Yuki. She banishes this card, "Zero Sprite", "Fiend Rose", "Mystical Space Typhoon", and "Grinder Golem" from her Deck from play via the first effect of "Spell Chronicle". Later Yubel activates the third effect of "Spell Chronicle" to make Jaden select one of the five cards banished by "Spell Chronicle". Jaden selects "Zero Sprite", so the latter is added to Yubel's hand. In the next episode, Yubel activates the third effect of "Spell Chronicle" to make Jaden select one of the four remaining cards banished by "Spell Chronicle". Jaden selects "Fiend Rose", so the latter is added to Yubel's hand. In the following episode, Yubel removes two Chronicle Counters on this card to make Jaden select one of the three remaining cards banished by "Spell Chronicle". Jaden selects "Mystical Space Typhoon", so the latter is added to Yubel's hand. On the last turn of the Duel, Yubel activates the the third effect of "Spell Chronicle" to remove its two Chronicle Counters on this card to make Jaden select one of the two remaining cards banished by "Spell Chronicle". Yubel assumed that Jaden was going to select "Grinder Golem", but Jaden selects "Super Polymerization" instead, so the latter card is added to Yubel's hand. Yubel then activates "Chain Material" to let her banish monsters in her field, hand, Deck, and Graveyard and use those monsters as Fusion Material Monsters when she performs a Fusion Summon this turn. After choosing twelve monsters (which were "Grave Squirmer", "Giant Germ", "Chaos Core", "Phantom of Chaos", "Dark Summoning Beast", "Infernal Incinerator", "Maju Garzett", "Lava Golem", "Infernal Flame Emperor", "Raviel, Lord of Phantasms", "Gate Guardian", and "Yubel - The Ultimate Nightmare") each with a consecutive Level from 1 to 12, Yubel activates this card to banish her twelve selected monsters from her Deck and field in order to Fusion Summon "Super Fusion God" (whose Summoning would unite the twelve dimensions into one), but Jaden activates "Spiritual Fusion" and selects to use "Super Polymerization" to fuse his soul with Yubel's. By doing this, Jaden frees Yubel from the Light's influence and unites her with the Supreme King forever. This card then went back into Jaden's possession since "Yubel" was fused with him.
- In episode 172, this card is shown in a flashback Crystal Beast Sapphire Pegasus has when he reminds Jaden and Jesse that they have overcome the darkness in their hearts.
- In episode 177, Jaden uses this card during his Duel against Nightshroud. He uses this card this card to discard "Winged Kuriboh" and fuse "Neos" with "Yubel" (who Nightshroud Special Summoned from Jaden's Deck to his side of the field via "Darkness Outsider") in order to Fusion Summon "Neos Wiseman".
- Yuri uses this card against Alexis Rhodes in episode 123 to fuse his "Ancient Gear Reactor Dragon" (which Alexis had taken control of with the effect of "Cyber Angel Natasha") with "Ancient Gear Golem" and "Ancient Gear Wyvern" to Fusion Summon "Ultimate Ancient Gear Golem". Alexis attempted to activate the effect of "Fusion Destruction" in response (which would have negated the activation of this card and inflicted 300 damage to Yuri, enough to win Alexis the Duel), but Yuri explains that this card's effect prevents cards and effects from responding to its activation.