The young player is greeted by Master Eon, the last protector of the realm, and he quickly explains that Skylands need their help. The Radiant Isles was the tranquil home to the Mystic Seekers, until The Darkness arrived and brought in a fearsome invader from the Outlands: Hektore. Using the power of the Darkness, Hektore enslaved the Seekers and forced them to build the Dark Mirror, which Hektore uses to shroud the Radiant Isles from the rest of Skylands to keep the power of the Seekers for himself. Master Eon then gave the new Portal Master the main objective: lead the Skylanders to destroy the Dark Mirror and free the Radiant Isles.

The young Portal Master is then teleported to an area where the leader of the Mystic Seekers, Fargus, and his son, Wendel, were awaiting for the new Portal Master's arrival, having escaped from Hektore. Before Fargus can start explaining on what to do next, evil laughter filled the air as Hektore has rediscovered Fargus and Wendel and was homing in on their location. In his haste, Fargus gave the new Portal Master the task of gathering Radiance Crystals, rebuilding the Shattering Sigil and destroy the Dark Mirror before he giving the title of the Last Free Seeker to Wendel. As Hektore arrived, Fargus sacrificed himself to protect Wendel and the new Portal Master from Hektore's wrath, being recaptured in the process. Shortly afterwards, both Wendel and the new Portal Master retreat to the Sanctuary, the only area in the Radiant Isles where Hektore can't reach.