Taking place 1000 years after the Legend of Spyro series, Cynder breaks Spyro from the bowels of the Earth to appear in the land of Equestria. Confused and lost, the two dragons struggle to befreind the local population, and are quite surprised over Celestia's kindness to them.

But as dragon sightings in Equestria begin to arise, history of the purple one is revealed, unravelling a 1000 year secret which Celestia has kept fom young Twilight and Equestria for as long as she has ruled. What is Spike and Twilight destined for? Why are dragons coming to Equestria? And who is Harmony?