Pandora is the last hope of humanity, which faced extinction due to years of conflict between the Humans and the Shades, a race of shadow like huminiods that feed off of life energy. In a desperate attempt to save their species the humans created Pandora, a massive storage device that will hold all of humanity in stasis until a time when it is safe to come out.

Pan a young man had agreed to be the key to unlocking Pandora when that time comes and he was then put into a separate container away from Pandora to await the day when Pandora needs to be activated.

Many years later following the events after A Canterlot Wedding, Chrysalis queen of the changlings has lost everything. Her hive is dead and she is left alone to wander the Everfree in loneliness. She soon stumbles upon Pan's stasis tank and agrees to help him save humanity. Now the two must face danger after danger as they try to uncover the secret of Pandora and the key to humanities salvation.