(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.

Beast of Gilfer
In Beastly Badlands (Mission 6) go west (not directly west) of the mountains aboveTower Pegasis. Beat him, The Illusory Gentleman and Neck Hunter

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)

Mystic Horseman+Hane-Hane+Man-eater bug
In Fury of the Empire(Mission 2)They are in the Forest south of Croethe. (Not directly south) Defeat them all and you get them all

Octoberser
In Mission 5, go south (not directly south) of Jokhan. Fight him and win to unlock.

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

Silver Fang
In War Campaign (Mission 1) He is directly in-between Jukhud and Makhad. Defeat him and you get him.

Suijin
Walk through the bay in Scorched (Mission 14) on Yugi Side, there, defeat him, Fortress Whale 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.

The Illusory Gentleman
In Beastly Badlands (Mission 6) go west (not directly west) of the mountains above Tower Pegasis. Beat him, Beast of Gilfer and Neck Hunter to get him

Time Wizard
Liberate Research Guild in Spellcaster (Mission 11) to get him

Winged Dragon Guardian of the Fortress #1
In Strategy (Mission 3) Go North of Dyethuro in the Mt.s with Yugi. He'll join you without a fight. You must send Yugi!!!!

Kaiba Side Monsters
These are a two of the Monsters avialale from the Kaiba Side Story Mode.Unlockable How to Unlock

Berfomet - "Hand of Fire" Go from the main base straight to the opponents.

Ryu-Kishin Powered - "Hand of Fire" Take over the enemy main base.