An ancient evil known as Discord escapes from his stone prison, and Twilight and her friends discover that the Elements of Harmony have been stolen. They need to retrieve them in order to save Equestria from eternal chaos, but first have to contend with Discord's sinister mind games.
With her friends corrupted by Discord and all of Equestria falling into disarray, Twilight is still determined to find the Elements of Harmony. But even after obtaining them, can the group defeat their foe before their friendship unravels completely?
When Twilight Sparkle forgets to write her weekly report for Princess Celestia, she becomes overly concerned over the potential consequences, and becomes increasingly stressed while trying to find a friendship-related problem she could solve and write about before day's end.
On Nightmare Night (a Halloween-like holiday devoted to the legends of Night Mare Moon), Twilight Sparkle tries to help a frustrated Princess Luna recover from bad karma from her time as Night Mare Moon.
When Rarity's sister Sweetie Belle stays at her house while her parents are on vacation, the two sisters get caught in conflicts and quarrels. However, when Rarity learns about the "Sisterhooves Social", an event themed around sisterly unity, she tries to quickly make amends with Sweetie Belle.
When visiting Zecora's hut to receive medicine for her chipped tooth, Apple Bloom finds a "Heart's Desire" flower which can make "talent come into view." When Apple Bloom believes it could help her finally discover her special talent, she instead becomes afflicted with the "Cutie Pox", which causes various Cutie Marks to appear on her body, and forcing her to continually perform the talents they represent.
After seeing the rest of her friends out in the park on a "Pony Pet Playdate", Rainbow Dash (with the help of Fluttershy) tries to find herself a flying creature to be her pet using a series of contests. However, Fluttershy insists that a tortoise compete in the competition as well.
Rainbow Dash gains a rise to stardom after becoming Ponyville's hometown hero. However, her new fame is threatened when a masked pony arrives, saving the day and taking over the spotlight. Just who is this mysterious mare in disguise, and how is she beating Dash at every turn?
Rarity runs into the upper-crust society of Canterlot and, by hanging out with them, becomes one of the popular ponies in the kingdom. She soon becomes distracted from preparing for Twilight Sparkle's birthday party, an event that she promised to attend. However, when Twilight's party is rescheduled next to a fancy garden party she had just been invited to, Rarity must decide whether to continue her rising social status or stay loyal to her friends.
It's Spike's birthday, and he is thrilled to receive more gifts than he could have ever hoped for. It is not long before his appreciation soon turns to greed, giving him an all-consuming obsession to hoard anything and everything he can lay his claws on, with a growth spurt to match. Can the ponies prevent their dragon friend from becoming a full-fledged monster?
Twilight Sparkle and friends participate in a pageant about the founding of Equestria; where conflicts between the Earth ponies Chancellor Puddinghead (Pinkie Pie) and Smart Cookie (Applejack), the unicorns Clover the Clever (Twilight Sparkle) and Princess Platinum (Rarity), and the Pegasi Commander Hurricane (Rainbow Dash) and Private Pansy (Fluttershy) attract Windigoes, spirits of the winter who feed off anger and hatred and bring coldness to those who do not show friendship.
When Diamond Tiara "sympathizes" with Apple Bloom spending time with her Granny Smith, during the harvest of rare Zap Apples, the young filly becomes embarrassed of her wacky methods. Things become much worse when Tiara suggests that the elderly mare attend their school's weekly Family Appreciation Day. Apple Bloom calls upon her fellow Crusaders to prevent this.
With no one to babysit their newborn twins, Mr. and Mrs. Cake reluctantly ask an overeager Pinkie Pie to watch them while they run a last-minute errand. However, as they leave, Pinkie will learn the hard way that playing with the kids and taking care of them are two different things.
When Applejack refuses to return to Ponyville after a major rodeo, she also refuses to explain why she wouldn't come back, which aggrevates her friends when they discover her working at another ranch.
Cider Season has come once again and the Apple family is ready to make their famous cider, but supplies are always frustratingly limited. But this year, twin stallions calling themselves the Flim Flam Brothers arrive to show off their new invention, the Super Speedy Cider Squeezy 6000 promising to make more cider in half the time. When they refuse to share business with the twins, the Apple family is instead challenged to a contest. Can Applejack, Granny Smith, Apple Bloom and Big Macintosh pull through and defeat the machine, especially with Sweet Apple Acres on the line?
When Rainbow Dash recovers at a hospital after a stunt flying accident, she becomes hooked on reading "Daring-Do" novels. However, she is afraid to admit to her friends that she enjoys reading, particularly because she previously viewed it as an "egghead hobby".
The Cutie Mark Crusaders try to use a love potion to create a relationship between Cheerilee and Big Macintosh after hearing she didn't have a "very special somepony" for Hearts and Hooves Day. However, the Crusaders quickly regret their decision after discovering that the potion recipe was connected to an incident where a Prince and Princess were affected by the potion so much that they couldn't perform their duties, causing the fall of their kingdom.
Pinkie Pie tries to become friends with new Ponyville resident Cranky Doodle Donkey. However, the donkey absolutely refuses to become friends with her, no matter how hard Pinkie Pie tries.
Iron Will, a rugged Minotaur, hosts a seminar teaching the ways of assertiveness. And who better to be in desperate need of it than Fluttershy. After being pushed around one too many times, she decides to take the self-help guru's advice and finally becomes more confident and even intimidating than she ever was before. In the end, will she take her new attitude too far when facing her friends?
Twilight gets an ominous warning from an unexpected visitor: her future self, but her curiosity prevents her from receiving the full message. Now she is forced to figure out what the messenger wants her to stop before it becomes inevitable.
Spike goes on a journey of self-discovery by joining the “Great Dragon Migration.” Does a rough and tumble gang of teenage dragons really hold the key to the questions Spike has about his identity?
Fluttershy struggles to overcome her fear of public humiliation so she can help Rainbow Dash and the other pegasi create a tornado powerful enough to lift the water required for rainy season in the cloud-producing city of Cloudsdale.