You'll need to do a bunch of things:

IN PONYVILLE: Activate all six Harmony Stones and get to the quest where Nightmare Moon arrives (""Mare in the Moon"" quest). Then, hit the ""GO"" icon for that quest!

IN CANTERLOT: Defeat Queen Chrysalis and her army of Changelings... then host the wedding of Princess Cadance and Shining Armor!

IN SWEET APPLE ACRES: Help the Apple family restore Sweet Apple Acres.

IN CRYSTAL EMPIRE: Help Shining Armor and Princess Cadance to restore Crystal Empire to its former glory and defeat King Sombra.

IN EVERFREE FOREST: Return the Elements of Harmony to the Tree of Harmony to heal it -- and save Ponyville from the invasion of the Everfree Forest! Then defeat Tirek, returning the magic he stole to Equestrians everywhere.

IN CHANGELING KINGDOM: Unite Thorax, Trixie Lulamoon, Starlight Glimmer and Discord, then defeat Queen Chrysalis and save everypony in Equestria!

IN KLUGETOWN: Help the Mane Six and their new friends to restore Klugetown after the Storm King's reign!