Ep.1: You, as a Guardian from the universe of Destiny, were ordered to check out some out of the ordinary readings in an area known as "The Skywatch." As soon as you make it, you find that the readings have just disappeared completely. A portal opens below you, taking you to The Crystal Empire.
Ep.2: You are introduced to The Mane Six, as well as Shining Armor, Princess Cadence, Spike, and Flurry Heart. An alert is sent out that King Sombra has returned to attempt to steal The Crystal Heart once more, and that he is aware of the ponies' tricks from their previous encounter. You offer to help them defeat Sombra, and you find yourself fighting one of the most dangerous forces of evil you face in Equestria.
Ep.3: After the fight with Sombra, you and The Mane Six find a way to get yourself back to where you came from. Twilight remembers the mirror that once took her to the human world, and suggests that you try to go through it to get back to your universe. You take her up on her offer and you say your last goodbye's before your trip home.