Continuing where the last one left off, the Doctor, the Wondercolts, the Dazzlings, and the Shadowbolts are pulled into a parallel pocket universe, dubbed the 'Shadow World,' a flip-flopped, upside-down version of the city of Canterlot, created by the Guardian of the Void.
With the Guardian's plan virtually unknown, the Doctor must bring together the conflicting teams, and stop the Guardian, as well as escape the Shadow World.