Jonouchi was controlled by Marik Ishtar for most of the Duel, and initially fought against Dark Yugi. After a few turns, Yugi, believing himself to be capable of returning Jonouchi to his former self, took over from Dark Yugi.
The Duel was set in such a way that the losing player would be dragged to the bottom of the sea. It was intended, by Marik, as a means of defeating and killing Dark Yugi. However Yugi's restoration of Jonouchi's mentality and the resulting DRAW led to the survival of both participants.
Marik Ishtar got his Rare Hunter underlings to keep an eye on Yugi and Dark Yugi's friends, Katsuya Jonouchi, Anzu Mazaki, Ryo Bakura and Sugoroku Mutou, during the preliminary stages of the Battle City tournament. He first alerted Dark Yugi of this after he Dueled him through the Doll and warned him that he had better find them before something bad happened.
Marik traveled to Domino City Aquarium, where he hoped to subject Jonouchi to his Millennium Rod's mind control powers. However he was interrupted by Dark Bakura, who agreed to help Marik defeat Yugi, in exchange for the Millennium Rod. Dark Bakura injured his host, Ryo Bakura, who then received aid from Marik, under the alias "Namu", allowing Marik to earn the trust of Jonouchi and Anzu. Shortly afterwards, Marik, brought them into contact with the Millennium Rod, allowing him to brainwash them. He implanted his own hatred in Jonouchi, making Jonouchi completely loyal to him and living to kill Dark Yugi.
Following the Explosive Tag Team Match of Death, Marik possessed Mask of Light to inform Dark Yugi that he had his friends ready for the next phase of his plan, where Dark Yugi was to Duel Jonouchi on the Stage of Death. Kaiba was interested in seeing how Dark Yugi, who had strong philosophies in unity, would cope when forced to battle a friend. When Kaiba was collected on his helicopter, he brought Dark Yugi with him to Jonouchi's then location, Domino Pier.
At the pier, Marik instructed two of his Rare Hunters to improve Jonouchi's Deck, by loading it with illegal direct damage cards. Capable of controlling his "dolls" with the Millennium Rod from a distance, Marik departed to the location of the tournament finals, leaving Jonouchi and Anzu under the supervision of his Rare Hunters.
When Dark Yugi arrived, he discovered that Jonouchi had been brainwashed. He made unsuccessful attempts to snap Jonouchi out of it, but Jonouchi challenged him to a life or death Duel. As Jonouchi led Dark Yugi to the stage for their Duel, Marik spoke through Anzu and advised Dark Yugi to cooperate or he would force Anzu to swallow a suicide capsule.
Dark Yugi and Jonouchi were handcuffed to a 300 kg (about 660 lbs) anchor hanging from two cranes above their stage. A bomb, set to detonate 15 seconds after a player's Life Points dropped to to 0 or 40 minutes after the beginning of the Duel, was attached to the anchor. Once detonated, the bomb would release the anchor, dragging anyone cuffed to it to the bottom of the sea. In order to survive, a player would have to defeat their opponent, which would unlock a box containing a key to their handcuff. They could then use the 15 seconds to free themself.
As Marik did not want the "Slifer the Sky Dragon" card to be pulled into the water, Jonouchi ordered Dark Yugi to take it out of his Deck. The card was in a box attached to his belt, rather than his Deck. As he removed the belt, he took the "Red-Eyes Black Dragon" card, which had previously belonged to Jonouchi, from the box and added it to his Deck.
1st turn: Dark Yugi
2nd turn: Jonouchi
3rd turn: Dark Yugi
4th turn: Jonouchi
Jonouchi commented on Dark Yugi playing a "wall" monster, noting that while the shield may be big, it would not stop a fireball. He activated "Hinotama", another banned card, directly inflicting 600 damage to Dark Yugi (Dark Yugi: 2500 → 1900 Life Points). As Jonouchi laughed, Dark Yugi promised himself to not give up and to win Jonouchi's heart back.
5th turn: Dark Yugi
6th turn: Jonouchi
Jonouchi thought that playing "Kuriboh" in Attack Mode was suicide and guessed that Dark Yugi had decided to die in order to save him. However Dark Yugi insisted that he would not die and would not let Jonouchi die either.
"Alligator Sword" attacked "Kuriboh", but Dark Yugi activated "Spellbinding Circle", immobilizing "Alligator Sword" and reducing its ATK ("Alligator Sword": 1500 → 800 ATK). Jonouchi was not too off put, as he stated that he was fighting Dark Yugi not his monsters. He then activated another "Hinotama" (Dark Yugi: 1900 → 1300 Life Points).
Dark Yugi asked if Jonouchi could not feel pain in his Duelist's heart. Jonouchi had no idea what he was talking about. Dark Yugi explained that the pain he was feeling was not from being burned by Jonouchi's cards, but from seeing him lose his heart as a Duelist.
Yugi began to speak with Dark Yugi. He said that he had never felt Dark Yugi hurt so much before and offered to halve the pain, by asking if he could Duel Jonouchi instead. Explaining that Jonouchi had always helped him before, even by risking his life, Yugi wanted to take his turn to help Jonouchi. Dark Yugi objected that the Duel was too difficult and was more like fighting Marik than Jonouchi. Yugi understood and reminded Dark Yugi that he had once said that Yugi's wish for friends had been fulfilled by his own endeavor not by the Millennium Puzzle. He wanted to prove that in this battle, by getting back Jonouchi's heart. Dark Yugi accepted but said that he would take over if Yugi's life got to be in serious danger.
7th turn: Yugi
Yugi introduced himself as Jonouchi's new opponent, much to Marik's displeasure. Marik wished to kill the pharaoh and would not be satisfied with simply killing the "vessel". He had Jonouchi order Yugi to bring Dark Yugi back, but Yugi said "too bad" and began his turn.
Yugi's hand contained "Red-Eyes Black Dragon", "Card Destruction", "Exchange" and "De-Spell". Before Summoning "Red-Eyes Black Dragon", Yugi wanted to make sure that Jonouchi's true self remained. He asked Dark Yugi to remain quiet while he made his next move. Yugi activated "Exchange", so both players were to show each other their hands and take a card from their opponent.
Jonouchi suspected Yugi's hand must only contain junk, but was surprised to see "Red-Eyes Black Dragon". Marik had been under the impression that Yugi was inexperienced and now thought he was even more foolish than he had suspected, as he was giving away a rare card, so easily. Marik commanded Jonouchi to take "Red-Eyes Black Dragon". However Jonouchi hesitated and following some internal struggling, took "Card Destruction" instead. He insisted that he did not need any Monster Cards and that "Card Destruction" was sufficient to crush Yugi. Yugi took "Magic Arm Shield" from Jonouchi.
Yugi declared that he knew for sure that Jonouchi had not lost his heart as a Duelist. He reasoned that Jonouchi had promised to not use "Red-Eyes Black Dragon", until his Duel with Dark Yugi and that was why he could not take it. Jonouchi claimed that was nonsense and told him to shut up.
Yugi Sacrificed "Kuriboh" and "Big Shield Guardna" to Summon "Red-Eyes Black Dragon". He asked if Jonouchi could see that the dragon's eyes had been stained with the color of sadness. He announced that he and "Red-Eyes" both wanted Jonouchi to by himself again and would fight if necessary.
8th turn: Jonouchi
Jonouchi declared that he would keep using illegal Spell Cards, until Yugi was dead. Dark Yugi grew concerned and wanted to take over, but Yugi took off the Millennium Puzzle, removing Dark Yugi's ability to take control. Despite having learned courage from Dark Yugi, Yugi still felt cowardly at times and needed to handle this himself in order to overcome that. Dark Yugi objected that Yugi could die and that the situation required incredible skill. Yugi agreed, but trusted Jonouchi and thought that if he did not become stronger by himself, Dark Yugi would never be able to leave him.
Jonouchi activated another "Hinotama" (Yugi: 1300 → 700 Life Points).
Concerned by the threat "Red-Eyes Black Dragon" posed, Jonouchi Summoned "Rocket Warrior". He used its power to transform itself into a rocket and deal 1500 damage to "Red-Eyes" via an attack ("Red-Eyes Black Dragon": 2400 → 900 ATK). Marik laughed that it was now just a dying dragon with 900 ATK and nothing to fear.
Yugi made his way across the stage and gave Jonouchi the Millennium Puzzle. He did not want it to sink to the bottom of the bay and asked that Jonouchi hold on to it when the time comes.
Marik thought that it was foolish of Yugi to hand over his most precious possession and figured it was evidence that he had given up. Marik ordered Jonouchi to take the puzzle apart and throw the pieces into the sea, fulfilling his revenge for 3000 years of slavery in his clan in the name of the pharaoh. Jonouchi removed a piece and prepared to throw it away. However this reminded him of a similar scenario, where he had thrown a piece of the puzzle away before, in the events leading up to him becoming friends with Yugi. Jonouchi struggled with conflicting feelings and eventually put the piece back on the puzzle.
When Marik asked how he could disobey him, Jonouchi replied that he is a Duelist, that he had no interest in revenge or what happened 3000 years ago and that he was going to settle this in a Duel. Vexed by the defiance, Marik decided to not let Jonouchi live, after winning the Duel.
9th turn: Yugi
With Marik's brainwashing gradually wearing off, Yugi felt his plan was going to work. With 14 minutes left before the bomb was due to detonate, he began his turn.
10th turn: Jonouchi
Marik thought that Yugi had made a foolish mistake, by leaving the weakened "Red-Eyes Black Dragon" in Attack Mode. Jonouchi drew "Panther Warrior" and Marik thought this was perfect, because if "Panther Warrior" could defeat "Red-Eyes" they would win.
Jonouchi Summoned "Panther Warrior" and "Rocket Warrior" switched to its rocket form. Marik ordered Jonouchi to eliminate "Red-Eyes". "Panther Warrior" began to attack, but Jonouchi had it target "Beta" instead. Yugi activated "Magic Arm Shield", the card he had taken from Jonouchi with "Exchange". "Beta" held onto the shield, whose magic arm gripped onto "Rocket Warrior", making it the new target of the attack. "Rocket Warrior" was not destroyed and dealt 1500 damage to "Panther Warrior" ("Panther Warrior": 2000 → 500 ATK).
11th turn: Yugi
Yugi Sacrificed "Beta the Magnet Warrior" to Summon "Archfiend of Gilfer" and used "Archfiend of Gilfer" to attack and destroy "Rocket Warrior" (Jonouchi: 3100 → 2400 Life Points). Jonouchi still remained under Marik's influence. Yugi thought that "Red-Eyes" was the only monster capable of doing anything about it, but it was too injured to even stand up.
As there was only 10 minutes left, Kaiba grew anxious and decided he must take a risk and intervene.
12th turn: Jonouchi
Yugi asked Jonouchi reminded Jonouchi of the promise he made after Duelist Kingdom, wherein to makeup for taking the prize money, Jonouchi would owe Dark Yugi one until the day he beats Dark Yugi. This caused Jonouchi to have flashbacks from the time of Shizuka Kawai's eye operation, which had been funded by the money and the time he promised to Duel Dark Yugi.
Jonouchi forsook Marik's order again and continued to Duel, Setting "Skull Dice" and "Graceful Dice".
13th turn: Yugi
"Archfiend of Gilfer" attacked "Panther Warrior", which Jonouchi had left in Attack Mode to lure Yugi into attacking. Jonouchi activated "Skull" and "Graceful Dice", targeting "Archfiend of Gilfer" and "Panther Warrior", respectively. Yugi used "De-Spell", negating the effect of "Graceful Dice". A 1 was rolled for "Skull Dice", so it had no effect. "Archfiend of Gilfer" destroyed "Panther Warrior" in battle (Jonouchi: 2400 → 700 Life Points).
With both players on equal Life Points, Yugi considered the possibility of them both escaping if their Life Points went to 0 at the same time.
With 3 minutes and 49 seconds left, Kaiba decided to take action. He drew the top card from his Deck, hoping it would be a common card, but got "Blue-Eyes White Dragon", which he immediately flung at the Rare Hunter holding Mokuba. The card became lodged in the Ghoul's hand, causing him to drop his knife in pain. Mokuba broke free and Kaiba attacked the two Rare Hunters, took back his card and forced both hunters into the water. He then ran towards the stage.
14th turn: Jonouchi
Jonouchi drew "Meteor of Destruction", another direct damage card, capable of expunging the remainder of Yugi's Life Points. Marik told him if he wanted to beat Yugi bad enough, he could play the card and spare his own life. He urged him to play the card, step out of Yugi's shadow by killing him and then have the Duel branded into his memories. Struggling with his inner conflicts, Jonouchi finally told Marik to shut up and that he did not want to have that in his memories. Slightly taken aback, Marik said to do nothing in that case and die happily together with Yugi, when the time runs out.
Yugi called out to Marik and declared him the true loser of the Duel. While Marik could implant evil thoughts in Jonouchi's mind, Yugi believed that Jonouchi would not give in. He remained convinced that he could turn Jonouchi back to normal in the one remaining minute. He exclaimed that when he achieves that, even if he and Jonouchi both die, Marik will have the fact that he lost burned into his memories forever. With little time left, he urged Marik to give him his best shot.
Marik reciprocated, issuing another command to Jonouchi to play "Meteor of Destruction". Jonouchi resisted, but Marik pushed all his vengeance into the card, forcing Jonouchi to play it. Jonouchi then snapped free and yelled at Yugi to not die. Yugi smiled and replied that he would not. He activated his "Mystical Rift Panel", allowing him to choose the target of "Meteor of Destruction". Marik became enraged, thinking Yugi was about to win.
Jonouchi back to his former self, asked why they were fighting. Yugi removed his Duel Disk and happy to see Jonouchi back, informed him that the Duel was just over and that they were not really fighting each other. Yugi clarified that Jonouchi had been fighting Marik's influence, while he had to fight himself to ensure he remained friends with Jonouchi. With 12 seconds left, he admitted to playing "Mystical Rift Panel" to buy the time needed to thank Jonouchi for teaching him courage and that he was not alone and to say that Jonouchi was his best friend and he loved him.
In the final second, Yugi choose himself as the meteor's target, reducing his Life Points to 0, giving Jonouchi access to his key. Before falling unconscious, Yugi told Jonouchi to use the next 15 seconds to unlock himself. However Jonouchi refused to leave Yugi and run. He noticed "Red-Eyes Black Dragon" and asked it to attack him. "Red-Eyes" complied and Jonouchi's Life Points also dropped to 0, opening the box containing Yugi's key.
With 2 seconds before the anchor dropped, Jonouchi took off the Millennium Puzzle and his Duel Disk. With no time to get his own key, he swung from the chain attaching him to the anchor over to Yugi's side of the stage and grabbed Yugi's key, just as the bomb released the anchor. While both players were pulled underwater, Jonouchi used the key to unlock Yugi's cuff and let him float to the surface. He apologized to Yugi and called him a real friend. Seeing that the key would not fit his own handcuff, Jonouchi suspected he had reached the end of his life.
On the surface, Mokuba pulled Yugi out of the water and reported that he was unconscious, but alive. Kaiba then picked up the other key and laughing that Jonouchi must now be at his limit, dropped it into the water for Jonouchi. Thinking he was about to die, Jonouchi spotted the key and freed himself.
Yugi woke up shortly before Jonouchi surfaced. Kaiba admitted to saving Jonouchi only because he admired his stupidity in forgetting to take his key, while in haste to remove his Duel Disk. He silently thought to himself that Jonouchi was finally a decent Duelist. Jonouchi was annoyed to have been saved by him, but said that he owed Kaiba one.
Jonouchi apologized for what happened, but Yugi told him not to blame himself, as he had succeeded in protecting what was important to them.
Anzu dropped the suicide capsule and Marik released control of her for the time being. She was unsure what she had been doing, but was greeted by Yugi and Jonouchi who were happy to see that she was okay.
The following cards appeared in this Duel:
- ↑ Yu-Gi-Oh! Duelist Duel 118: "Attack that Opponent!"
- ↑ Yu-Gi-Oh! Duelist Duel 125: "Arena of Death!!"
- ↑ Yu-Gi-Oh! Duelist Duel 119: "Each Other's Duel!"
- ↑ Yu-Gi-Oh! Duelist Duel 122: "Conquer the Sea!!"
- ↑ Yu-Gi-Oh! Duelist Duel 124: "The Reason for Dueling"
- ↑ 6.0 6.1 Yu-Gi-Oh! Duelist Duel 131: "Where Jonouchi Waits"
- ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 Yu-Gi-Oh! Duelist Duel 134: "Heart Attack!!"
- ↑ 8.0 8.1 8.2 Yu-Gi-Oh! Duelist Duel 132: "The Place of Destiny"
- ↑ 9.0 9.1 9.2 9.3 9.4 9.5 9.6 9.7 9.8 Yu-Gi-Oh! Duelist Duel 133: "The Unwanted Duel!!"
- ↑ 10.0 10.1 10.2 10.3 10.4 10.5 Yu-Gi-Oh! Duelist Duel 135: "The Card of Pride"
- ↑ 11.0 11.1 11.2 11.3 11.4 11.5 11.6 11.7 Yu-Gi-Oh! Duelist Duel 137: "The Last Piece of the Puzzle"
- ↑ 12.0 12.1 12.2 12.3 Yu-Gi-Oh! Duelist Duel 136: "Yugi Fights Alone"
- ↑ 13.0 13.1 13.2 13.3 13.4 13.5 13.6 13.7 13.8 13.9 Yu-Gi-Oh! Duelist Duel 138: "One Card of Life and Death!"
- ↑ 14.0 14.1 14.2 14.3 14.4 Yu-Gi-Oh! Duelist Duel 139: "Friends till the End"
- ↑ 15.0 15.1 15.2 15.3 15.4 Yu-Gi-Oh! Duelist Duel 140: "The Treasure"