In the start, the player is in his room with Joey (Jounouchi). The Player, Joey, and Yugi are going to a duelist competition. Joey organizes his Deck, and asks the player how he is. The player gets two choices. Whichever he chooses doesn't affect the plot. Joey gets excited and talks about the duel competition, but Yugi isn't there yet and Joey gets impatient. Suddenly Yugi enters and informs them that his Millennium Puzzle has disappeared along with Yami Yugi (Dark Yugi). So then Yugi and Joey follow the player outside (They will follow him for the majority of the game). Téa (Anzu) waiting at the Clock Tower Square and is shocked by the bad news, but it gets even worse. Ishizu appears reporting that all Millennium Items have disappeared and asks the player for help in saving the world from a Dark Being, Reshef. To resurrect him, it is necessary to gain the power of all three Egyptian God Cards that turned into stone.
Before leaving the player can check out the other duelists to win some extra cards. When he tries talking to Téa, she'll leave the Clock Tower Square wishing him the best. He may even go to Truesdale's (Sugoroku's) card shop to buy some cards or challenge Duke (Otogi) and Tristan (Honda) outside or Yugi and Joey inside the shop.
If the player heads over to KaibaCorp (this is optional), he'll see Rebecca trying to reclaim one of Kaiba's "Blue-Eyes White Dragon" cards because he had torn-up Truesdale's one. To prove to Kaiba that she's worth dueling, the player has to face her. After defeating her she will leave. Now the player can duel the KC DuelTek 1000. It can be found right from the statue in the middle of the three Blue-Eyes White Dragons. Before dueling it, the player can chooses from the following:
- "Novice": This is pretty easy. The computer's cards are not hard to beat.
- "Standard and above": When this is chosen the player must choose from the following:
The Egyptian ExhibitionEditTo achieve your first goal you have to head to the Duel Express which is currently located in the Domino Station. To enter the train stage you have to enter Domino Station. Now answer the controller's question with "Yes". After that, you and either Yugi or Joey will duel against two of the controllers that want to test your abilities. You may choose to pick either Joey or Yugi to team up with you (it doesn't matter any of them will win).
Right after defeating the controllers, PaniK (Player Killer of Darkness) arrives and follows you into the train. But before entering the Duel Express itself, you may want to reinforce your Deck by dueling the four duelists in front of it. But if you just want to continue the story you can enter the Express by talking to the controller. Once you've entered the train, talk to the far left steward. The train will depart. The first wagon is a duel wagon where you can duel the two passengers and the controller you already talked to.
Now head over to the next car and meet PaniK. He'll challenge you and after that the Express arrives the Egypt Exhibition. If you want to power up your Deck head to the left car first before leaving the Express, and challenge the young lady with the red ribbon and her father.
Now follow PaniK and talk to the guy standing in front of the door at the end to pass and enter a dark room where some artifacts are stowed away.
As you enter, you see PaniK losing his consciousness. The other guy standing in front of him is the Millennium Items Keeper that now wants to prove your worthiness to gain the Millennium Necklace. After defeating the keeper the necklace is handed over to you. At the same time it brings you a vision: The world's final doom! And Yami's watching it!
Outside the room back at the express station, you have to meet the Kaibas. after that, leave the Exhibition by following the yellow line to the upper left exit of the controlling station and head back to Ishizu who is waiting at the Clock Tower Square. When you try to talk to her, a mysterious looking guy with a violet carpet appears. He calls himself the Puppeteer of Doom (Ventriloquist of the Dead) and challenges you to a duel.
After defeating him, he'll give you a special invitation card from his master Sol Chevalsky. Put it in your duel disk to view the video saved on it. It will give you the location of the next Millennium item: Domino Pier.
Domino PierEditChallenge the guy that is admiring the yard with his girlfriend before going on board.
Inside you see Jean Claude Magnum, head to Mai and help her out by defeating him, After doing so, talk to Mai. She gives you information on a mysterious cargo on this yard. Duel the other lady to get one more rare card.
Now head to the cargo bay, there you will found the Millennium Items Keeper. you have to duel him, after defeating him you will receive the Millennium Key. Shadi appears to tell you that every Millennium Item carry its bearer's memories.
Head back to Ishizu to get the next location. When you show her the Millennium Key, Slifer the Sky Dragon regains its power! She wants to give it to Yugi but he refuses because Slifer would belong to Yami, so you get the card instead.
ItalyEditWith Slifer on your side you can now travel to Italy. Another Millennium Item should be buried there somewhere. Head to the next screen and speak to Bonz. Defeat him, then Bandit Keith arrives along with his accomplices Strings and Rare Hunter. He tells you that he has control over them and that they call themselves the "Neo Ghouls". After the "Neo Ghouls" leave Bonz shows you a hidden room where the Millennium Items Keeper awaits to test you.
If you defeat him, he'll give you the Millennium Ring. The spirit of the Ring Yami Bakura (Dark Bakura) appears to proclaim a world of chaos.
The next item will be found in China.
ChinaEditA guy will welcome you, Head to the next screen at the right and talk to the other guy who's standing in your way. It doesn't seem that he would let you pass, so return to the first screen. Challenge the guy at the snack bar, it will revealed that he's Para, then the other guy will arrive and reveal that he's Dox. They challenge you in a tag duel. Kaiba and Mokuba arrive to help you, you will have to select one of them to duel him and Kaiba will duel the other.
After you've defeated either Para or Dox you may now pass the blocked way to reach the Millennium Items Keeper. If you defeat him, he'll give you the Millennium Eye that shows you Sol Chevalsky.
Get back to Ishizu. As Obelisk The Torementor regains its power, Kaiba appears to reclaim the card. After Seto and Mokuba leave, Serenity comes and says she wants to see the Kaibaman Show.
Free TimeEditSo it seems that you and your friends may spend a little time for yourselves. Go to KaibaCorp to enjoy the show. In front of the building you'll see the Big Five begging Mokuba to rehire them.
You may now act as a part of the Kaibaman show when you face the "Big Bad Five" disguised as Deepsea Warrior, Nightmare Penguin, Jinzo, Judgeman and Robotic Knight. after you defeat them they form up the F.G.D, so you need the help of Kaibaman. Then Roland dressed up as Kaibaman appears. He Summons Black Luster Soldier and Blue-Eyes Ultimate Dragon, He then fuses them to form up the Master of Dragon Soldier. He attacks and destroy F.G.D ending the show.
When you return to Ishizu, she gives you the next location: Canada
CanadaEditGet inside the cave and talk to Rex Raptor (Ryuzaki). After defeating him he'll let you pass deeper into the "Dungeon". The Millennium Items Keeper is waiting in there to prove your worthiness. Defeat him to get the Millennium Rod that lets Marik's memories appear to tell you that Marik himself is living in Egypt. The cave starts shaking, so Joey wants to leave.
Go back to Ishizu to learn the next location: The Galappagos Islands.
Galappagos IslandsEditWhen you enter you will find Mako (Kajiki). If you want you can duel him several times to get some rare cards. To complete the story, advance more, you will find Weevil (Haga), again. If you want you can duel him, if you didn't just enter the ruins. Inside the ruins, you will find Yami Yugi in front of the Millennium Scales. But after a long conversation it is revealed that he is not Yami Yugi but actually Mimic of Doom (Mimic of The Dead), Once you defeat him you will obtain the Millennium Scales. Shadi again appears to ask you to save Pegasus for he's a victim of Reshef's dark power.
If you head back to Ishizu and talk to her, Slifer loses his power and turns back into stone again. Ishizu's shocked because she thought that the power of the Millennium Items you gathered would resurrect The Winged Dragon of Ra. It is obvious that Kaiba's Obelisk might also have turned back into stone so Ishizu begs you to look for him while she would chase for the mightiest Millennium Item: The Millennium Puzzle.
The Neo Ghouls are comin'EditYou don't have to go a long way to find Seto and Mokuba. They're at the KaibaCorp. building. Talk to him, no matter what option you choose, Seto will leave.
If you return to the Clock Tower Square you'll watch two Neo Ghouls attacking some lower duelists. Chase them away by defeating them.
At the upper right part of Clock Tower Square, Hanasaki dressed up as Zombyra the Dark is trying to get rid of one of the Neo Ghouls but he fails and the Ghoul leaves. Whenever you try to talk to him, a Neo Ghoul comes to you to challenge you.
When you reach the place where you usually would meet Ishizu, you'll see another cut scene, Rare Hunter in a Duel with Espa's younger brothers, and he summons Exodia to defeat him. Right after the duel ended, Espa Roba (Esper Roba) himself appears to defend his brothers. They notice you, and Rare Hunter challenge you to a duel while Espa takes on the other Neo Ghouls.
Defeating him should be quite easy, I don't think he'll be able to summon Exodia just in time. Thanks to Jinzo, Espa is able to do away with the other two Neo Ghouls. From Espa, you learn that Ishizu was kidnapped by the Neo Ghouls and brought to the Domino Station.
Get there. But the Neo Ghouls would not let you pass, so you have to duel one of them but if he leaves another Ghoul takes his place. You'll have to draw them off the train stations somehow.
It's time to ask your duel friends for help...
Need of helpEditFirst, you should go Domino Pier to help Mai out of her misery.
For this you have to get rid of Arkana (Pandora). As soon as you drove the Ghouls away, Mai will thank you and leave to do what she can to defeat the Ghouls at the Clock Tower Square...
The next ally is Mako who's still on the Galappagos islands, in the island's ruins. There you'll have to face Strings to make Mako go to Clock Tower Square.
Weevil can be found in China, Bonz in Italy, and Rex in Canada. Beat the Ghouls to help them out.
Now finally go back to Clock Tower Square and talk to Espa Roba. There are still some Ghouls in the town that you have to defeat. You'll have to face Rare Hunter at the Kaibaman Show while Esper Roba taking on the Big Bad Five. But be careful, because this time he's much harder to beat than last time.
Afterwards, you'll be able to head to the Egyptian Exhibition but you're still not able to get there directly. So you'll have to take Duel Express which has been taken over by the Neo Ghouls. They are no big deal to defeat because of their lowered Life Points. After you have forced your way through the carriages, the Express arrives at the Exhibition station.
Deal with the three Neo Ghouls and move towards the chamber you already were. As you meet Kaiba, talk to him so that you can reach it. Hand over the Millennium Items to Keith to save Ishizu. Keith will resurrect The Winged Dragon of Ra but he just resurrects the Sphere Mode. As you beat Keith, Slifer will rise again and the Millennium Puzzle is given back to Yugi.
Keith receives Ra's judgment. As a reward you get "The Winged Dragon of Ra (Sphere Mode)". Yugi and Yami's reunification does not last for long. Reshef takes control over Keith and smashes the Puzzle into many pieces.
Para appears and steal one part of the puzzle so Yami again is trapped inside his item. At the station you'll meet Seto who is forced to watch as Mokuba is kidnapped by Dox. Para comes out of the room and the two brothers leave with Mokuba inviting Seto to visit Pegasus.
Now you need to meet Paradox to find out where Sol's castle is located...
ParadoxEditAs you enter the Chinese area Paradox appears in front of you. He tells you that Ra would not be able to help you if he is in Sphere Mode, so you need to find someone who can activate Ra's battle mode.
Head back to Clock Tower Square and ask Ishizu to find out that the only one who could help you is her brother Marik (Malik) who lives by now in Egypt. When you arrive, Odion (Rishido) welcomes you. On command of Marik he lets you pass if you choose the first option, he'll duel with you if the second option is your choice.
Marik will surely help you but he has to test your abilities. Afterwards, if you beat Marik he'll awaken Ra's battle mode. However Marik is not able to resurrect Ra's invincible Phoenix Mode. He asks you to return if you found out the secret behind that Mode.
Now return to Paradox but before you are able to gather any information from him you have to play a game with him.
Now here comes the most complicated part of the game. Head right to the next screen. The guard blocks your way until you've beaten him. After you defeats him he gives you a second card as reward and if you want to get inside the room you just enter the screen again and the guard blocks the way again.
It's not that complicated as it looks like. Just duel until you received Kuriboh, Time Wizard, Giant Soldier of Stone, Celtic Guardian and Curse of Dragon in order so you can get in.
But before Paradox is providing any information, you have to do a little quiz:-
Which card you obtained first?
Which was the fifth?
Curse of Dragon.
Then he'll challenge you. After defeating him, he'll provide you with the location of Pegasus's hideout.
Before moving to his hideout, you might want to get Ra's Phoenix mode.
Head back to Truesdale's shop and enter the following code into the Password Machine:51404976
Now head to Egypt where Odion welcomes you. You tell him that you've found out the secret of Ra's Phoenix mode. He leads you to his master Marik who will transform Ra into its Phoenix mode.
By now you should be prepared for the final quests. Be careful, as the opponents you face from now on will start to have a Life Point advantage at 10000 rather than the usual 8000.
Pegasus IslandEditEnter the cable railway to follow Kaiba. But it's a trap! Three of Pegasus Servants attack you so you have to duel them. After leaving the cable railway, PaniK awaits you and Mimic of Doom supports him. You and Joey will face them. But they won't disappear so Joey himself will take on the two of them, leaving you and Yugi to continue on.
Go right to see the World Map and enter the Dungeon.
DungeonEditWhen you enter the dungeon you may choose whether to go left or right, it doesn't really matter. There are just two enemies you can't walk around.
After you reached the stairs at the top of the dungeon, two other duelists appear, Para and Dox. You and Yugi have to defeat them but if they're defeated they will not free the way. So Yugi frees it for you by dueling both on his own.
Now you're alone...
Pegasus CastleEditAs you want to enter the castle, Paradox appears and tells you that you'll need five spirit cards from your friends to be able to pass the labyrinth that awaits you. So head to Mako, Mai, Weevil, Espa Roba, Bonz and Rex to duel them. They will give you their dearest cards: The Legendary Fisherman, Harpie Lady, Insect Queen, Jinzo, Pumpking the King of Ghosts and Two-Headed King Rex. (They can be found where you met them in the first place).
After you've gathered the required cards you may proceed to enter the castle.
You'll meet several Pegasus Servants that are disguised as your "fellow duellists" as Paradox would say. First you have to battle Bonz, as second comes Rex, and then comes Weevil, followed by Mako, Espa Roba and Mai.
After defeating Sol's Servants that are disguised as Bonz, Weevil, Rex, Maik and Mako, right before entering the room where you meet Kaiba, you can turn left and enter a hidden room. Look at the large picture so that Shadi appears. He'll tell you what happened to Pegasus after Yami Bakura defeated him and took his Millennium Eye if you choose "Yes".
Entering the room is neither necessary for completing the game nor lets you enter a different storyline though seeing Shadi will clear up the story a bit more.
Now you'll be able to watch Kaiba defeating one of the servants. Ishizu also arrives and asks Kaiba for help but he's still thinking he will beat Pegasus with his perfect Deck. Mokuba suddenly shows up under Reshef control and wants to challenge Seto but he is not able to harm Mokuba. So it's up to you to bring back Mokuba and beat him.
Once Mokuba regains his senses, Seto thanks you. But although he owes you his help, he will not give you his Obelisk until you beat him in a duel.
The Final BattlesEditNow after defeating Kaiba you will face Sol Chevalsky. Take caution - he starts with 20000 Life Points. Once you defeat him, Reshef will be released. Drawing on the despair from the many duelists you defeated to get this far, Reshef will prove to be overwhelming. However, Kaiba, Yugi and Joey will show up to offer encouragement, along with weakening Reshef with their signature cards so that you can face him. You will then need to defeat Reshef, who boasts an initial 40000 Life Points and holds all 3 God Cards, without a chance to recharge your Life Points.
After defeating Reshef, he tries to regain strength by drawing on Sol Chevalsky's soul. Sol Chevalsky will have none of it, but as Reshef has an unbreakable grip on his soul, Chevalsky opts to become the new vessel in which Reshef will be sealed, and calls on the player to use the power of the 3 God Cards to seal Reshef within him. After Chevalsky's sacrifice, the player and his party escape Chevalsky's collapsing hideout.
Peace returns to the world and Domino City as all the player's friends part ways. Ishizu Ishtar returns to, once again, ask for the return of the God Cards so that they will be sealed. After the player does so (without much of a choice here), the end credits roll.
Hall of EternityEditAfter you beat the game, you can re-load your last save and a new location on the world map will be opened, the Hall of Eternity. In the Hall of eternity you can find some of the hardest duelists in the game, each of which, upon defeat, yields some of the most powerful cards in the game, along with a massive (by this game's standards) 10-20 increase in Deck Capacity.
Duelists in The Hall of Eternity
- Maximillion Pegasus - Starts with 30000 LP
- Seto Kaiba - Starts with 60000 LP, possesses Obelisk the Tormentor.
- Dark Joey - Starts with 30000 LP
- Yami Bakura - Starts with 60000 LP
- Yami Yugi - Starts with 60000 LP, possesses Slifer the Sky Dragon.
- Yami Marik - Starts with 60000 LP, possesses The Winged Dragon of Ra.
- Noah - Starts with 60000 LP
- Shadi - Starts with 30000 LP
- Paradox - Starts with 30000 LP