Waking the Dragons Story 6 : Waking the Dragons , known as Story 6 : Doma the Dark Organization ( ６ のドーマ " Sutōrī Roku : Yami no Soshiki Dōma " ) in the Japanese version , constitutes season 4 in the " Yu - Gi - Oh ! Duel Monsters " anime . This story arc is exclusive to the anime , being one of two arcs , not based on the manga , created to fill the gap between the Battle City and Pharaoh ' s Memories arcs . The name Doma comes from the storyline ' s central antagonists , Doma . It is sometimes referred to by fans as the Orichalcos arc , named after " The Seal of Orichalcos " , a card central to the storyline of this arc . Appearances . Games . Winners are in bold . Game mechanics . Unlike the anime - exclusive Virtual World story arc , the story arc does not introduce any new gameplay elements ; instead , it is notably the first time that Fusion Monster s were permitted to attack on the turn that they were Summoned , which was prohibited by the Battle City Rules . As in the Battle City and Virtual World arcs , both players start a Duel at 4000 Life Points , and monsters can be Normal Summon ed in face - up Defense Position . Instead , the arc features many new cards , such as the " Legendary Dragon s " and Dartz ' s " Orichalcos " cards , which offer new game mechanics . Plot . The storyline is based around an organization ( named Doma in the Japanese version ) which uses a card known as " The Seal of Orichalcos " to entrap the souls of people and duel monsters alike , in an effort to revive an ancient dragon monster known as The Great Leviathan . The beast was the center of the destruction of Atlantean society 10 , 000 years ago , well before the time of the Egyptians ( on which the rest of the series is based ) . In the past , the Great Leviathan was defeated by the three Legendary Dragons : Timaeus , Critias , and Hermos . Although not destroyed , the Leviathan was severely weakened , forcing Dartz , King of Atlantis , and his Doma organization to collect souls for 10 , 000 years . Dartz knew that he would succeed after seeing the power of Pharaoh Atem in Ancient Egypt some thousands of years later ( in the English adaptation , Dartz cites the Shadow Realm specifically ) . Stealing Yugi ' s Egyptian God Cards . The story begins after the end of the Battle City tournament , when Atem wanted to recover his lost memories by using the Egyptian God Cards to activate the chamber of the Nameless Pharaoh King inside the Memory World . Suddenly , a dark force freezes the Tablet of Lost Memories , sealing it to prevent him from doing so . Outside , Duel Monsters have come to life and began attacking the civilians without warning , even after Kaiba shut down the Dueling system . When the monsters kept appearing , he called Industrial Illusions in an attempt to get help . Later that night , a group of perpetrators broke into the Kame Game Shop and stole the three God Cards from Yugi ' s grandfather Solomon Muto , who had been given the cards for safekeeping . Giving chase to the thieves , they eventually encounter Gurimo , a mysterious man in a cape . Gurimo is collecting souls , and plans to collect the souls of duelists by defeating them in a duel . To this end , he uses " The Seal of Orichalcos " card , a Field Magic Card that could not be dispelled and prevented outside interference , with only the winner of the Duel being able to escape and the loser having his soul taken by the Seal . Although Gurimo manages to unleash the power of " Obelisk the Tormentor " against its former owner , Yugi eventually wins the Duel but ultimately fails to recover the God Cards . The God Cards eventually arrive in the hands of Dartz , who sacrifices their power to awaken his Great Beast , The Great Leviathan . Releasing the Legendary Dragons . The next night , as the world sees a giant eye in the sky , Yugi and the Pharaoh awaken in the depths of the Millennium Puzzle where they encounter " Kuriboh " , urging them to follow a portal hidden inside the puzzle to the world of beasts . There , they are greeted by " Dark Magician Girl " , who tells then the tale of The Great Leviathan , and urges them to pull a sword from an ice statue . They do so , and unlock the power of " The Eye of Timaeus " , who proceeds to destroy the eye in the sky above the world of beasts . Similarly , Yugi would unleash the same power in the real world , forcing The Great Leviathan to retreat . The other two Legendary Dragons would also be unleashed in a similar manner - " Fang of Critias " was unlocked by Seto Kaiba in a Duel , after kowtowing to a demand allegedly by Maximillion Pegasus to Duel at his Duelist Kingdom as a publicity stunt . There , he discovers that one of the thieves , Amelda ( Alister named for Aleister Crowley , who coined the unicursal hexagram that acts as the symbol of the Orichalcos , in the English version ) , had led him there , wanting retribution for what KaibaCorp had done against his family . Although " The Seal of Orichalcos " was indeed used , the battle was fought to a DRAW , allowing both Alister and Kaiba to escape unharmed . The third Legendary Dragon , " Claw of Hermos " , would be unlocked by Joey Wheeler ( Katsuya Jonouchi ) : when Yugi and his friends receive a video from Pegasus ( as it turns out , shortly before he is defeated and his soul sealed ) , who implores Yugi and his friends to travel to America and retrieve a card holding the key to defeating their then - unknown threat . At Pegasus ' Industrial Illusions HQ however , they are locked inside the building , where Mai Valentine ( Mai Kujaku ) emerges to battle Joey . During this Duel , Yugi and friends discover that Mai had been wandering the Earth after their Battle City tournament ; although she finished in the top 8 , she was always overshadowed by Joey , and continually traumatized by her loss to Marik Ishtar ( in which she was physically and emotionally seriously scarred ) . Determined to become stronger at any cost and never wanting to lose another Duel again , Mai eventually wound up with Dartz , eagerly accepting his offer of becoming stronger , not realizing that the power of the Orichalcos would be her undoing . The change in Mai ' s behavior would , as it turns out , be partially due to Valon , the second of Doma ' s three Swordsmen , who had cared for Mai in her time of need , and wanted her to move on with her life by defeating Joey ( effectively also doing his work for her ) . When Joey appears to have the upper hand in the Duel ( thanks to " Claw of Hermos " ) , Valon uses his Orichalcos Stone to break the seal , rendering the match a no - contest and allowing both Mai and Joey ' s souls to survive . Meanwhile , Duke Devlin ( Ryuji Otogi ) , accompanied by Weevil Underwood ( Insector Haga ) and Rex Raptor ( Dinosaur Ryuzaki ) , would manage to break into the building and unlock the doors . Seto and Mokuba Kaiba would also appear , and all of them would help Yugi find the card that Pegasus claimed would help Yugi end the threat of Doma - yet , when they find it , it is blank . Yugi ' s sacrifice . The third swordsman , Rafael , would later challenge Yugi . Rafael claimed that Yugi and his friends are fighting for the wrong cause , and that Rafael was a noble hero out to save the world . He claimed that mankind was inherently evil , and that the Orichalcos exposed the darkness within the souls of mankind - thus the need for them to be sealed by " The Seal of Orichalcos " . However , as Yugi Dueled , he finds himself easily outmatched by Rafael ' s Guardian Monsters , which he refused to allow to go to the card Graveyard . After Rafael plays the Spell Card " Exchange " , Yugi finds himself with " The Seal of Orichalcos " in his hand . Not wanting to lose yet not wanting to play the Seal , the two souls of Yugi would debate over whether to use the card . Blinded by the desire to win at any cost , Yami ( in control of Yugi ' s body during the Duel ) ignores Yugi ' s pleas and plays the Seal in order to power up his monsters . Using the ability of " Catapult Turtle " , he sacrifices monster after monster to wear away at Rafael ' s Life Points , even sacrificing his trusted " Dark Magician " and " Dark Magician Girl " in the process . Yet , Rafael is able to survive and use the situation to his advantage by Summoning " Guardian Eatos " . Eatos would use the spirits of Yugi ' s own monsters to defeat Yugi . As the Seal slowly circles around the fallen Pharaoh , however , Yugi realizes that two souls reside within one body , and allows the Seal to take him instead , sacrificing himself so that the Pharaoh would survive . Meanwhile , Weevil and Rex , after seeing the power of the Orichalcos , seek to have the power for themselves . Fighting the darkness . The Pharaoh , despite the attempts of his friends to cheer him up , became distraught over the loss of his other self . Meanwhile , as the Pharaoh and company continue to travel , Weevil and Rex meet Dartz , who grants them the power of the Orichalcos . In return however , they are told to use their newfound power on the Pharaoh and Joey - a win - win scenario for Dartz in any event . The two would manage to hijack the train the Pharaoh and company would be riding in - Weevil isolating Yami and Téa Gardner ( Anzu Mazaki ) , while Rex finding Joey and Tristan Taylor ( Hiroto Honda ) . Thus , the two Duelist Kingdom rematches were slated to begin , only with much more on the line . While Joey would have little trouble dispatching Rex with the help of his " Claw of Hermos " , Timaeus would seemingly abandon the Pharaoh , forcing him to win the Duel without it because of his recent action he did when Dueling against Refael . He would ultimately prevail against Weevil with the help of " Breaker the Magical Warrior " , which , along with its ability and " Berserker Soul " , allowed it to attack Weevil repeatedly as long as the Pharaoh drew and discarded monsters - which he did ruthlessly . Téa would implore the Pharaoh to stop - long after he had beaten Weevil - just as Yami was about to discard " Dark Magician Girl " . Just then , however , the moving train would head off a cliff , although they would survive , having been rescued by a mysterious person . His savior would be revealed as Ironheart . Ironheart would lead the Pharaoh to the Valley of Lost Souls , where he found the spirit of Yugi . Yugi confronts the Pharaoh , and implores him to face himself through a Duel if he is really sorry for his misdeeds in his previous Duel , with both players sharing the same Deck . In this Duel , Yugi would bring forth " The Seal of Orichalcos " , and would use a similar strategy to what the Pharaoh had used against Rafael ; sacrificing monsters to win . The Pharaoh would protest against Yugi ' s strategy not to make the same mistake he did or it will prevent him from saving him and humanity ; but , Yugi , under the influence of Orichalcos , only sees him as an evil individual who never cared about everyone but himself and cruelly makes him pay for his own action . However , the Pharaoh ultimately wins the Duel after successfully countering Yugi ' s moves . Despite not wanting to lose Yugi again , the Pharaoh promises to save him . Just as he was about to leave , however , Dartz , who had been observing the Pharaoh ' s activities , conjures a spell to bring forth an Orichalcos Soldier . While Dueling the Orichalcos Soldier , however , the Pharaoh realizes that Timaeus is his only hope of winning , yet he cannot use it as he does not have the card in his Deck ( after having given it to Ironheart , believing him to be unworthy of the card ' s power ) . Ironheart and his family ( consisting of grand - daughter Chris and pet wolf Skye ) would sacrifice their lives to deliver the card to Yugi , who uses it successfully to defeat the Orichalcos Soldier . With the darkness within himself eliminated , the Pharaoh could finally move on , and hope to find and rescue Yugi , wherever he may be . Alister ' s loss to Critias . Each of the three swordsmen were chosen for their apparent misfortunes in life - all of which , as it turns out , was orchestrated by Dartz . " Alister " came from a war - torn region , and his life revolved around helping himself and his brother survive the ravages of war . Ultimately , however , his family was killed ( " captured " in the English adaptation ) by opposing forces , who were allegedly funded by Kaiba Corporation . Holding its head , Gozaburo Kaiba responsible , Alister seeks his adopted sons for revenge . He manages to hijack the plane Seto and Mokuba were piloting , and seeks a rematch with Seto to end it once and for all . As the Duel moves on , Alister recounts his history with the Kaiba Corporation , and notes that whether he wins or loses , the plane will crash , allowing " The Seal of Orichalcos " to claim all three lives . Kaiba , willing to protect Mokuba at any cost , would use Critias to prevail . On the last turn of the Duel , Alister gave in so that Mokuba would not lose his brother as Alister did . In his brief moment of defeat before being claimed by the Orichalcos , Alister sees a bit of his brother in Mokuba , allowing him to stop living in the past and move on with his life . Valon ' s loss to Hermos . " Valon " was a child delinquent , always getting into fights . When he gets into a fight with a gang of street thugs , they retaliate by burning a local church down , along with a nun who had taken care of him . In revenge , he had killed the street thugs , and as a result , he was sent to prison ( this detail was omitted from the English adaptation - there , Valon was framed and imprisoned for a crime that was orchestrated by Dartz ) . He was sent in and out of twelve detention centers , before a warden turns him to Duel Monsters . There , the warden sets forth a Battle Royale style challenge , where the winner would be set free . Valon would eventually be the winner , having trapped all others within " The Seal of Orichalcos " . He is granted release , into the custody of the prison ' s " sponsor " - Dartz . Valon , in his perspective , saw Joey as the big obstacle in Mai ' s life , and vowed to take him down in her honor , while Joey wants to take down Valon , believing that Doma is to blame for turning Mai against him . When their Duel inevitably begins , Valon uses his Deck of Armor Monsters - mostly 0 ATK and mostly 0 DEF monsters with devastating effects , to literally form a suit of armor around himself , intending to literally beat Joey senseless . Likewise , Joey is forced to defend himself with a suit of armor of his own , formed from his trusted " Red - Eyes Black Dragon " . The two would physically punish each other throughout the match , with Joey coming out in front . The Duel between Valon and Joey would arouse Mai ' s interest , and Joey would be forced to Duel her in order to set the record straight . Joey , tired and physically beaten from the previous Duel , is unable to concentrate on the Duel , yet manages to deal serious damage to Mai - yet , he manages to reach out to her just as Joey is about to lose . Mai would ultimately not attack Joey ( and win the Duel ) , but Joey collapses in exhaustion , allowing " The Seal of Orichalcos " to take his soul . Taking the fallen Hermos with her , she proceeds to confront Rafael , the last of the three swordsmen , where it is implied that her soul was also taken . Rafael ' s loss to Timaeus and Hermos . " Rafael " came from a well - off family , which was taken from him when they were separated from each other at a young age . He was the sole survivor of a luxury liner disaster , and washed up ashore on a deserted island ( the English adaption mentions that his family had survived the shipwreck , but had completely forgotten about Rafael ) Rafael would live on the island for three years ( according to Rebecca Hawkins ) , with his Guardian cards the only thing allowing him to retain his sanity . His attitude in Dueling was simple - as the cards had cared for him during those years , he would try to do the same to his monsters . When he was eventually rescued , he found that the world he lived in had changed . Unwilling to accept the outside world 9 years after the events of his accident before the events of the series , Rafael turned to Dartz . When Rafael confronts the Pharaoh again , he hands the Pharaoh " Claw of Hermos " ( which he had picked up from Mai ' s soul - less body ) , and promises to defeat the Pharaoh like he did before . This time , however , it is instead Rafael who uses the " The Seal of Orichalcos " , to the Pharaoh ' s horror ( up to that point , it seemed that Rafael was not the type of person who would use such a card ) ; after Timaeus destroyed Eatos , and like the Pharaoh before , Rafael would proceed to sacrifice his trusted Guardians , all to power up his deadliest Guardian , " Guardian Dreadscythe " - a guardian who could be revived simply by discarding a single card . Determined to set Rafael free , and see the errors of his ways , the Pharaoh takes it upon himself to destroy Dreadscythe by any means necessary , and he does so with the combined power of Hermos and " Guardian Eatos " - Rafael ' s most trusted Guardian . With Rafael seeing the error of his ways , he uses a final Magic Card to resummon all his Guardians , at the cost of the remainder of his life points . Though Rafael loses , his soul is surprisingly not taken since he found the light in himself , as souls are taken because of the darkness inside of someone . The final battle . Rafael proceeds to tell the Pharaoh and company where to find Dartz , and they proceed to Dartz ' s lair , where they find an entire room of captured souls . Dartz appears , and challenges the Pharaoh and Kaiba in a two - on - one match . Dartz , however , is more powerful than the three Swordsmen combined - not only is he able to repel the " Master of Dragon Soldier " , a fusion of two of Kaiba ' s and the Pharaoh ' s most powerful cards , but is able to expand the full power of " The Seal of Orichalcos " , by playing its 2nd and 3rd levels : " Orichalcos Deuteros " and " Orichalcos Tritos " . These would would give Dartz even more Life Points , making additional attacks fruitless . Furthermore , his array of " Mirror Knights " is making the Pharaoh reluctant to attack , as the souls of his fallen friends are trapped inside each one . When Rafael tries to intervene , he unleashes his stored - up rage at Dartz ( who at that point revealed that he was the source of Rafael ' s troubles in life ) , and " The Seal of Orichalcos " ( dormant since his earlier Duel ) takes his soul . Kaiba , however , sees past Dartz ' s tricks to throw the Pharaoh off guard , and proceeds to attack . By destroying his monsters , however , Dartz releases an even more powerful monster ( " Orichalcos Shunoros " ) , which easily defeats Kaiba and allows the Seal to claim his soul . Desperate for a comeback , Yugi manages to draw the blank card that Pegasus gave him - only this time , the card has changed to " Legend of Heart " , allowing the true nature of the Legendary Dragons to be revealed . In the past , the kingdom of Atlantis was guarded by three knights , which were turned into dragons and sealed away during the battles that eventually destroyed Atlantis . By using the " Legend of Heart " , the three Legendary Dragons revert to their true form , allowing " Legendary Knight Timaeus " , " Legendary Knight Critias " , and " Legendary Knight Hermos " to be reborn . The three Knights manage to destroy the three levels of " The Seal of Orichalcos " , as well as Dartz ' s " Orichalcos Shunoros " . However , Dartz has a last resort up his sleeves - by sacrificing all of his Life Points , he could Summon " Divine Serpent Geh " , which has infinite ATK and DEF , and also allow Dartz to continue to Duel as long as it remained on the field . Likewise , Yugi is forced to similarly entrust his own livelihood to his " Dark Magician Girl " . By combining all three Knights of Atlantis to form the " Timaeus the Knight of Destiny " , the " Divine Serpent Geh " is destroyed , winning the Duel in Yugi ' s favor . Although as a result , the souls of Yugi , Joey , and Kaiba are liberated from the Orichalcos , Dartz sacrifices his own soul , allowing the Great Leviathan to be revived and fusing himself with the Great Beast to control it . Attack of the Great Leviathan . The Great Leviathan has been reborn , thanks to Dartz ' s own sacrifice . Even the combined forces of the Knights of Atlantis and the most powerful of Yugi ' s , Kaiba ' s and Joey ' s monsters were not enough to stop it - their only hope , as it seems , was to put all their own power into reviving the three Gods of Egypt : " Obelisk the Tormentor " , " Slifer the Sky Dragon " , and " The Winged Dragon of Ra " . With the three monsters revived with the power of the light of all Dartz ' s prisoners this greatly reduces The Great Leviathan ' s strength , enough for the three Gods to easily destroy it , freeing all the captive souls in the process . Yet , The Great Leviathan would continue to exist , as it was made from the evil mind of the mankind . The Pharaoh , wanting to help Dartz be rid of the influence of the Orichalcos , takes it upon himself to personally ensure that the Great Leviathan , and the influence of the Orichalcos , is no more . With it gone Dartz returns to normal , and proceeds happily into the afterlife with Ironheart , Chris , and the rest of his family . As for the main characters , the Knights of Atlantis and " Dark Magician Girl " thank them for their assistance , and return to the world of the beasts . The three Legendary Dragon Cards , as well as " Legend of Heart " , disappear into thin air just as they came , vowing to reappear when the world is in danger again .