Unlock Joey
Win the story mode with both Yugi and Kaiba to unlock Joey.
Unlock Soul of Oblisk
To unlock the Soul of Oblisk, beat Yugi's story.
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.
Unlock Eye of Ra
To unlock the Eye of Ra, beat Marik while playing as Joey.
Unlock Silfer's Orb
To unlock Silfer's Orb, beat Kaiba's game.
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.
Konami Code Hijinks
Go to any empty space and press the Konami Code: UP, UP, DOWN, DOWN, LEFT, RIGHT, LEFT, RIGHT, B, A, and you'll hear a jokey sound.
Moisture Creature
The Moisture Creature is on Kaiba's mission, Sever The Supply. Send a team to Sweit, build a watch tower, then trace the circle. Search the east side of Sweit. You might him in a small pass between mountains. He is rumored to move around sometimes. Keep searching in that area and you should find him.
Octoberser
In Yugi's Story on the Turbulent Waters level, send someone down towards the base called Thor-Mount. About half-way down you will encounter the monster Octoberser. Win and it will join your army.
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 Silver Fang
After you beat Yugi's story (or maybe its after you beat the whole game) play Yugi's story again. On mission 1 send Yugi straight towards the enemy's main base and once you reach the forest you will find Silver Fang all by himself.
Challenge Mode
Defeat everyone at least once. When you go to 'Load Game', there will be a challenge mode with all of your items from the three stories.
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.
Busterblader
In Kaibas level Dragon'slair use z to send someone to Den and on the mountian you will find a busterblader and a cyber commander beat them and you will get them both.