Season 1

With Chad recovering from spine surgery, a new villain, the Admin, begins his conquest.

The Admin and his army, The Collective, launch an attack on the Spy Ninjas safehouse, while Melvin is at the grave of the former Project Zorgo Leader.

The Admin banishes the Spy Ninjas to his prison and the Warden forces Chad to work for him, while Melvin searches the safehouse for clues.

The Admin reminds Melvin Ginera of his defeat at the hands of the Project Zorgo Leader, and corrupts Melvin, but the Spy Ninjas do not realize and he infiltrates.

After narrowly escaping from the Admin's twisted prison, Chad and the remaining fugitives discover not just a forgotten city but an entire hidden world buried by The Admin.

Continuing their journey in search of home, the Spy Ninjas land in a world entirely controlled by the spirit of the Project Zorgo Leader.

The Spy Ninjas face the Technomancer, a general of the Collective, while the Admin launches an attack on Las Vegas.

The Collective launches an attack on the safehouse, while the corrupted Melvin resurrects the Project Zorgo Leader.

The Admin reveals that he was the one who corrupted the Project Zorgo Leader, and sent it to attack the Spy Ninjas.

The Admin continues his reign over the United States, while the Spy Ninjas are stuck in the headquarters of the Collective.

The Doppelganger joins the Spy Ninjas as his home was destroyed by the Admin, while the tyrant frees the lava zombies from the pyramid.

Chad learns how to use the new object, while the Admin prepares to take the form of Vy Qwaint.