One year after the events of Shattered Dimensions, Allen has returned to Equestria in hopes of peacefully living out his days with his friends, and plans on asking Princess Luna to marry him. Unfortunately, Allen's hopes are interrupted when Project G.E.M., a secret initiative from Earth, breaks the boundaries between the two dimensions, which subsequently awakens a warlord from the pony-human war thousands of years ago.

Now, Allen must deal with the threat of attacks from his new enemy, preparations for the upcoming Crystal Fair, and an unexpected visit from someone he never thought he would see again: his father, Robert Greathouse.