Completing Challenge Mode
Have Dark Magician, Dark Magician Girl, and Dark Magician #2. Level them up so that the Dark Magicians can use Dark Burning Magic. Equip Rageki and Mirror Force and Red Medicine or a Dien Keto Cure Master. You should not have a problem with challenge mode.
Get Obelisk The Tormenter
To get Obelisk the Tormenter, beat story mode once with Yugi Moto. He should appear as an item that you can summon once a round.
Get the Magician of Black Chaos
To get the Magician of Black Chaos, use the black luster ritual on the dark magician.
More Money
While playing, press Up, Up, Down, Down, Left, Right, Left, Right, A, B on an empty piece of land.
Rex Raptor
You can get Rex Raptor is after the battle with Weevil. He sends out about four warriors. After you defeat them, take him head on with two of your Marshals. He carries a Two Headed King Rex, Megazowler, and Uraby with him.
Unlock Alpha Warrior
On DREAM WORLD liberate MEMORY BRIDGE in the Yugi story.
Unlock Black Luster Soldier
When you get the Black Luster Ritual use it on Gaia instead on the Dark Magician to get the Black Luster Soldier.
Unlock Eye of Ra
To unlock the Eye of Ra, beat Marik while playing as Joey.
Unlock Joey
Win the story mode with both Yugi and Kaiba to unlock Joey.