In an alternate history of Equestria, the Elements of Harmony were destroyed and in their place Celestia created the secret intelligence agency known as Mane6.

Donut Joe, formerly known as Agent Con Mane, is brought out of retirement by MARE, the head of Mane6. Joe is asked to find out the whereabouts of his former partner, Strange Ways, who has gone missing in the island of Janeighca. Furthermore the barrier surrounding the New Lunar Republic is being attacked by black magic and the Lunar Intelligence Agency believe that the spell is originating from the Ponibean Sea. Joe works together with LIA agent Sky Blazer and a local Zebra to determine who is behind all of this. The culprit appears to be the reclusive owner of a forbidden island named Dr. Ironhoof. But Ironhoof has agents everywhere and Joe must keep on his hooves at all times in order to stop the mad Unicorn’s schemes.