Set after the events of The Glare of the Python episodes in Scroop's cannon series, Kairi is still having nightmares about how Clockwerk let Mang into Radiant Garden to turn Kanji into the crazy demonic cat lady Mirage. Spyro and the others are trying to help Kairi cope that Clockwerk is just a decent memory unknown to them that a mysterious old threat from the past looms over Kairi. It is Clockwerk himself still a ghost and he wants one thing on his mind....VENGANCE!!! Vengance against all of his enemies, starting with his former owner's daughter and a certain racoon theif who helped her and her misfit family defeat him since Kailass failed to carry out his plans.

Their first mission takes them to the Villain Leage still under Pitch and Chrysalis's leadership to seek answers about Clockwerk's return with Pooh and his pals tagging along and the Cooper gang following in secret after hearing about Clockwerk's major comeback and his revenge plans on Kairi. However, this quest to protect Kairi from Clockwerk's vengance has attracted the attention of Interpol and alcourse, Carmimilita Fox.