Taking place immediately after the events of Nightmare Moon's banishment to the moon, the capital city of Everfree lays in wait as a battle between the forces of the Queen of the Night and Princess Celestia draws to a close. Meanwhile, the princess herself, aided by her wise and enigmatic court wizard Starswirl the Bearded, undergo a secret endeavor involving the elements of harmony.

Seven years later, the new capital, Canterlot is in mid-construction, but that isn't going to stop the Princess from starting her school for gifted unicorns. One of them, Comet Winterspell, is particularly excited and nervous about his new life in a boarding school away from his home. As long as his loyal sister Snowflake is by his side, he should be fine. It isn't long though until a fire in Trottingham bordering the Everfree Forest launches a magical event of epic proportions, unleashing a power within the young colt even he was unaware of. The Princess takes notice of Comet and takes him under her wing as her pupil.

At one point within the next year, Comet stumbles across a book in the restricted center of the library labeled "The Elements of Harmony." All inquiries about this book are immediately dismissed by his superiors as fantasy and silly rumors. The colt however, remains convinced that there is a hint of truth to this story. 12 years later a tragedy hits all of Equestria: the moon refuses to rise. Riots break out and rebellion begins to stir as angry citizens accuse Celestia of purposefully holding it back. Meanwhile, a mysterious individual known only as Umbra begins to gain political foothold in both the ranks of the Loyalists and Rebels alike.

Comet takes this opportunity to seek out the answers he wants about the Elements of Harmony and sets off on a journey that will take him all across Equestria and introduce him to new friends and foes alike.