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.
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.
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.
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.
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.
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.
Unlock monsters (Yugi Side)
(Note: If you lose to any of these monsters, you wont be able to get them)
Aqua Dragon - Walk through the bay in Scorched (Mission 14) on Yugi Side, there, defeat him, Fortress Whale and Suijin to get them.
Baby Dragon - SouthWest of Beyzon in Refugees (Mission 8) with Joey to get him.
Dark Elf - Beat brainwashed Tea in Spellcaster (Boss of Mission 11) to get her.
Dark Magician (Arkana) - Defeat Arkana (Boss of Lost Cause, Mission 16) on Yugi side to get him.
Dark Magician (Yugi) - Defeat Panik (Boss of Beasty Badlands, Mission 6) on Yugi side to get him
Dark Magician - Girl Liberate both captured towns in Counter Attack (Mission 10) on Yugi side, having Dark Magician in Yugi's Team.
Fortress Whale - Walk through the bay in Scorched (Mission 14) on Yugi Side, there, defeat him, Suijin and Aqua Dragon to get them.
Harpie Lady - Ocupete West of Ce-Reizo in Break Free (Mission 9) to get him (You have to use Mai with the Harpie Lady Airo)
Panther Warrior - Defeat Joey (Boss of For That Someone Special) with Mai to get him.
Red Eyes Black Dragon - Defeat Joey (Boss of Phantom Blast, Mission 12) to get him
Sanga of the Thunder - West of Ce-Reizo in Break Free (Mission 9) to get him
Suijin - Walk through the bay in Scorched (Mission 14) on Yugi Side, there, defeat him, FortressWhale and Aqua Dragon to get them.
Summoned Skull - Get into Tower Pegasis in the Beasty Badlands (Mission 6) on Yugi Side, there, defeat him and he will join you.
Time Wizard - Liberate Research Guild in Spellcaster (Mission 11) to get him
Blue Eyes White Dragon (Kaiba's side only) - Beat the Lord of D. in the Burrow on level 14
Extra Challenge Mode - Play through all three stories
(Note: After unlocked, enemy monsters will not be the same as before)
Unlock the Egyptian Gods:
"Eye of Ra" - Beat Marik in Joey's Story
"Slifer's Orb" - Beat Kaiba's Story
"Soul of Oblisk" - Beat Yugi's Story
Black Luster - Ritual Beat the mission finishing Shadi in the Yugi Side
Black Luster Soldier - Use the "Black Luster Ritual" on Gaia the Fierce Knight
Dark Magican #2 - Defeat Arkana in the Yugi Mode
Gaia the Fierce Knight - Go to the middle of the lake in the Yugi Mission "Face Off"
Magican of Black - Chaos Use the "Black Luster Ritual" on Dark Magican
Unlocking Magician of Black Chaos and Black Luster Soldier
Run through yugi's chapter two times and aquire 2 Black luster rituals use them on gaia the fierce knight and Dark Magician
"Black Luster Ritual" - Beat the Shadi who has the item
"Black Luster Soldier" - Use Black Luster Ritual on Gaia the Fierce Knight
"Magician of Black Chaos" - Use Black Luster Ritual on Dark Magician