The Agents of Shadow is a secret organization of 13 warriors. They operate under General Phai, who takes orders from Lord Kala. Many have assumed friction between Kala and Phai. But this has been proven wrong. They fight using an unique battle system. They appear and challenge a member of Mario's team. Most of the time they challenge either a character or a partner to a duel. Defeating all Agents of Shadow is optional, and some such as Yozhi and Phai are required. But defeating all agents rewards the player with a special secret character. After the Agents of Shadow are exterminated, a short scene shows Phai and Sycho in a conversation, whoever they are never faced again. This could be a new game featuring the agents of Shadow once again, however this is just speculation.
List of Duels
| Agents of Shadow | First Combantant | Area | Result | Second Combantant | Third Combantant |
|---|---|---|---|---|---|
| General Phai | Mario | Yossy Island | 1/Victory 2/Loss 3/Loss | Bowser & Missile Mike | Mario |
| Missile Mike | Mario & Krystal | Yossy Island | Loses and joins Mario's Party. | None | None |
| Dye Guy | Mario & Timmi | Solomon's Ridge | Perhaps Death. | None | None |
| Haz-Mat | Goshi or Yoshi or Oshi | Jibber Jabber City | Defeated | None | None |
| Wrath Guy | Lakilester | Sprite Ocean | Defeated | None | None |
| Yozhi | Yoshi | Yossy Island | Defeated and Imprisoned | None | None |
| Sycho | Missile Mike | Ridge of Jajo | 1/ Defeated 2/Retreated, status unknown. | None | None |
| Dark King | Jumbo Kong | DK Island | 1/ Victory, 2/ Victory 3/ Defeated | Yoster | Izzy |
| T-Rex | Rawk Hawk | Solomon's Ridge | Defeated and presumably dead. | None | None |
| Boowzer | Lord Boo | Holo Cost, Mansion | Defeated | None | None |
| Blaze | Gaz | Goomba University | Defeated and Reformed | None | None |
| King KO | Kommando | Shroom City Skyscrappers | Defeated and presumably dead. | None | None |
| Black | Spike | DK Mountain | 1/Defeated and critically injured. 2/ victory 3/ Death | Spike | Lakilester |
Members
- General Phai
- Missile Mike - Reformed replaced by (Sycho) - Bullet Bill
- Dye Guy - Shy Guy
- Haz-Mat - Shroob
- Wrath Guy - Boo Guy
- Yozhi - Yoshi
- Sycho - replaced Missile Mike - Bullet Bill
- Dark King - Ape
- T-Rex - Rexe
- Boowzer - Boo
- Blaze - goomba
- King KO - Koopa
- Black - lakitu
