Twilight Sparkle, a ward of the crown ever since she accidentally turned her parents into plants, is dispatched by Queen Celestia to the small hamlet of Ponyville; the Unicorn has expressed fear that an eldritch Alicorn of the past will arise there. And when Twilight Sparkle fails to defeat the fiendish NightMare Moon in the two Queens' former palace of Concordia Arbos, the planet is plunged into night on one side and day on the other. With only shards of rock to her name and a band of ponies at her side, she sallies forth to bring back the Sun. She will traverse field and mountain, desert and labyrinth if she needs to. Will she be able to solve the mystery of the Elements of Harmony? Who was NightMare Moon, and what evils come to Equestria apart from her everlasting night? And why does Queen Celestia believe that making friends takes priority over everything else for Twilight...?

Can be found on TV Tropes.
Has a YouTube reading by our own Alchemystudent.

The Elements of Friendship, Book I: Harmony
The Elements of Friendship, Book IS [interlude one-point-five]: Bonds
The Elements of Friendship, Book II: Chaoskampf
The Elements of Friendship, Book IIS [interlude two-point-five]
The Elements of Friendship, Book III
The Elements of Friendship, Book IIIS [interlude three-point-five]
The Elements of Friendship, Book IIII

This story is a sequel to The Elements of Friendship, Book I: Harmony

After freeing Queen Celestia's sister from the pall of NightMare Moon, Twilight Sparkle has settled down in Ponyville with her new circle of friends. But no sooner does she settle down than a foe from the reign of NightMare Moon returns: Trixie Lulamoon! Bearing a mysterious trinket of great magical power, Trixie leads Twilight to test her assessment of friendship being the greatest magic. What is the Alicorn Amulet? How does it possess such absolute power? Where did Trixie get it from? Who gave it to her, and why? And what was the Sonic Rainboom, and how does it tie Twilight Sparkle to the friends she has just made...?

Can be found on TV Tropes.

The Elements of Friendship, Book I: Harmony
The Elements of Friendship, Book IS [interlude one-point-five]: Bonds
The Elements of Friendship, Book II: Chaoskampf
The Elements of Friendship, Book IIS [interlude two-point-five]
The Elements of Friendship, Book III
The Elements of Friendship, Book IIIS [interlude three-point-five]
The Elements of Friendship, Book IIII

This story is a sequel to The Elements of Friendship, Book IS [interlude one-point-five]: Bonds

Peace has found Equestria once more, and they have had their Queen of the Night returned to them! But a dark figure who looms over Equestria's past returns to the present: Discord. The chimerical despot over Equestria in a bleaker age threatens to throw the stable regime into a dominion of anarchy. Worse still, he has removed his one weakness, the Elements of Harmony, from the equation. How will Twilight Sparkle defeat the draconequus deity without the Elements of Harmony? How will her and her friends stay in unity without the Elements? And what connection does Discord have to Equestria's Queens...?

Updates on Wednesday afternoons.
Can be found on TV Tropes.

The Elements of Friendship, Book I: Harmony
The Elements of Friendship, Book IS [interlude one-point-five]: Bonds
The Elements of Friendship, Book II: Chaoskamπf
The Elements of Friendship, Book IIS [interlude two-point-five]
The Elements of Friendship, Book III
The Elements of Friendship, Book IIIS [interlude three-point-five]
The Elements of Friendship, Book IIII