Twilight's Kingdom

Princess Twilight Sparkle and her friends travel to the Crystal Empire, where Twilight is to help greet delegates from another nation. She finds this duty unfulfilling, and laments this to Celestia, Luna, and Cadance, unsure what her role in Equestria is. The other three assure her that her responsibilities will become clear in time.

Celestia has a vision revealing that an evil centaur named Lord Tirek has escaped from Tartarus and is now draining ponies of their magic. Gathering the other princesses, Celestia explains how they had stopped Tirek before and that they must stop him now before he becomes too powerful. The other princesses turn to an eager Twilight to deal with Tirek, but Celestia instead puts Discord in charge due to his ability to sense magical imbalances that will be caused by Tirek's activity. Twilight returns home to Ponyville, disappointed at being unable to help, and heads to the castle ruins with her friends in the Everfree Forest to catch up on studying. Discord interrupts them, teases them about his mission, and reminds them of the locked chest at the base of the Tree of Harmony (from "Princess Twilight Sparkle"). Twilight suspects there may be something to help against Tirek inside, and she and her friends search the books in the castle. Twilight realizes Discord mentioned their shared journal, and finds stories written by the other five where they were challenged in regards to their core Element of Harmony, and were able to help another, receiving an item in return. They gather these items, which transform into five of the six keys needed to open the box, but Twilight realizes that she has not yet faced a challenge similar to theirs and thus cannot provide the last key.

Discord encounters Tirek, but he tempts him with having freedom over friendship, so Discord decides to join forces with Tirek and reverts to his old ways. Twilight is summoned back to Canterlot, where Celestia reveals Discord's treachery and that Tirek now has his sights set on taking the princesses' magic for himself.

Celestia reveals that the best plan to prevent Tirek from getting the alicorn magic is to hide it away within Twilight since her recent ascension to Princess is still unknown to Tirek. They transfer their powers to Twilight, who has difficulty in controlling the power and avoids her best friends on returning to Ponyville while she practices control.

Tirek confronts the princesses and finds their magic gone. Despite this setback, he mocks that their plan is unable to change anything and banishes the three to Tartarus. He then expresses his gratitude for Discord's assistance by giving him a medallion as a sign of loyalty. As they discuss this, Tirek learns of Twilight's existence and sets off to Ponyville. With Discord's assistance, they trap Twilight's friends and Tirek steals their power. He then turns on Discord and takes his magic as well, having only used Discord as a pawn to become powerful as he tells him he is no longer useful to him. Tirek finds Twilight and when she tries to run away, he destroys the Golden Oak Library in Ponyville. Enraged, Twilight attacks Tirek and after a battle between the two superpowered beings, they realize they are evenly matched and Tirek offers to release Twilight's best friends in exchange for her magic. Twilight realizes this is the same type of situation that her best friends had previously experienced and agrees to the deal on the condition that her friends and Discord are freed. Tirek takes the alicorn magic and begins to go on a rampage.

Remorsefully, Discord apologizes to Twilight's friends for betraying them and gives Twilight the medallion Tirek had given him as a sign of his true friendship. Twilight recognizes this as the sixth key, and they quickly race to the box. With all six keys present, the box opens and powers the Tree of Harmony, causing Twilight and her best friends to be infused with a rainbow-like power. Together, they face Tirek, repulse his attacks and revert the magic drain. Tirek is weakened to his frail form and returned to Tartarus while Twilight and her best friends return the magic to all the other ponies in Equestria and free the princesses. The box is then sent by the Tree of Harmony into the ground at the edge of Ponyville, and grows into a tree-like castle. Celestia informs Twilight that since she is now the Princess of Friendship, her responsibility is to continue helping spread friendship across Equestria with the help of her best friends, including Discord.