Chancellor Puddinghead tries to pass a law mandating Earth ponies drink carrot juice at every meal. (Forgotten Friendship)
Clover the Clever undergoes seven trials, one of which involves pursuing and defeating an evil sorceress in possession of a memory-erasing artifact. (Forgotten Friendship)
A mysterious blizzard appears and "topples the tribes' precarious peace." The tribe leaders set out to find a new land. When they all discover the same land at the same time, their feud starts over, attracting the windigos and causing another blizzard. As the tribe leaders freeze, their cohorts become friends, and the Fire of Friendship is created. The tribe leaders thaw out of the ice, make peace, and agree to share the land as one unified race. Equestria is founded. (Hearth's Warming Eve)
During the "pre-Classical era," Star Swirl the Bearded creates more than two hundred spells and has a wing in the Canterlot archives dedicated to him. (Luna Eclipsed, It's About Time)
During the "Paleopony Period," a population of ponies is afflicted by cutie pox. Random cutie marks appear all over ponies' bodies, causing them to uncontrollably perform the talents that come with them. The cause of the breakout is never discovered, and the cutie pox disappears as mysteriously as it arrives. (The Cutie Pox)
An unnamed Earth pony prince gives an Alicorn princess a love potion/poison and starts Hearts and Hooves Day. (Hearts and Hooves Day)
Lord Tirek and Scorpan travel to Equestria, seeking to steal its magic. Scorpan, having come to appreciate the ponies' ways, betrays Tirek to the princesses. Tirek is banished to Tartarus for his crimes. (Twilight's Kingdom - Part 1)
Celestia and Luna are abducted by evil forces from another dimension, and Stygian and the Pillars join forces to rescue them. (Legends of Magic Annual 2018)
Stygian turns into the Pony of Shadows, and the Pillars of Old Equestria imprison him and themselves in limbo. Before trapping themselves, the Pillars plant a seed infused with their magic that will later grow into the Tree of Harmony. (Shadow Play - Part 1)
Princess Celestia and Princess Luna defeat Sombra, turn him to shadow, and banish him beneath the ice of the Arctic North. (The Crystal Empire - Part 1, My Little Pony: FIENDship is Magic Issue #1)
A curse enacted by Sombra causes the Crystal Empire and its population to vanish into thin air. (The Crystal Empire - Part 1, My Little Pony: FIENDship is Magic Issue #1)
Princess Luna becomes resentful when ponies sleep through her beautiful night. Her bitterness transforms her into Nightmare Moon, and she attempts to overthrow her sister for absolute control. Princess Celestia uses the Elements of Harmony to banish her sister to the moon. (Friendship is Magic, part 1)
Pear Butter marries Bright Mac and becomes a member of the Apple family. Grand Pear and the rest of the Pear family relocate to Vanhoover. (The Perfect Pear)
Current era
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Cadance is born a Pegasus pony in Canterlot and found in the woods by Earth ponies. When she grows up, she reverses a love-stealing spell cast by a pony called Prismia. Princess Celestia recognizes Cadance's abilities, transforms her into an Alicorn, and adopts her as her niece. (Princess Cadance, Royal Envoy, Twilight Sparkle and the Crystal Heart Spell)
Young Rarity makes costumes for a school play. As she suffers a creative block, her horn lights up and drags her off in an unknown direction. (The Cutie Mark Chronicles)
During a race against Hoops and "Dumb-Bell", Rainbow Dash creates a sonic rainboom, causing her cutie mark to appear and setting in motion a chain of events related to her future friends' cutie marks. (The Cutie Mark Chronicles)
At the start of the race, young Fluttershy—a considerably weak flyer—falls toward the ground and is saved by a swarm of butterflies. She quickly becomes enamored with the world on the ground. Rainbow's sonic rainboom frightens Fluttershy's new animal friends. When she calms them, her cutie mark appears.
Unable to fit in among the social Manehattan elite, Applejack becomes homesick. She sees Rainbow's sonic rainboom pointing toward Ponyville. She races home to reunite with her family, and she gains her cutie mark.
During Twilight's entrance exam to the School for Gifted Unicorns, Rainbow's rainboom causes Twilight's magic to temporarily overload. Spike is hatched from his dragon egg, Twilight obtains her cutie mark, and Celestia takes Twilight on as a personal student and protege.
Rarity's horn drags her all the way to a giant rock. Rainbow's rainboom causes the rock to split, revealing a deposit of gems. Rarity uses the gems for her school play costumes, and her cutie mark appears.
Young Pinkie Pie is dissatisfied with her life as a rock farmer. Upon seeing Rainbow's rainboom, she is overwhelmed with happiness and throws her first party, gaining her cutie mark.
The adult versions of the Mane 6 are transported to the past and meet their younger selves. In order to preserve history, Celestia seals away the memories of the younger ponies. (My Little Pony: IDW 20/20)
In unspecified chronological order...
Rainbow Dash moves to Ponyville on her birthday. (Pinkie Pride)
Pinkie Pie holds a party in Ponyville and inspires Cheese Sandwich to become a party pony. (Pinkie Pride)
Princess Celestia sends Twilight Sparkle to Ponyville to oversee preparations for the Summer Sun Celebration, despite Twilight's concerns regarding the 1000-year anniversary of Nightmare Moon's banishment.
Possible deviation: Chrysalis and the changelings succeed in taking over Equestria, driving many ponies away into hiding. (The Cutie Re-Mark - Part 2)
Twilight is invited to her brother Shining Armor's wedding to Princess Cadance.
Twilight rescues the real Princess Cadance from captivity, and Queen Chrysalis and the changelings are ultimately defeated by the power of Cadance and Shining Armor's love.
After a thousand years, the Crystal Empire reappears. King Sombra, in a weakened shadow form, attempts to regain control.
Possible deviation: King Sombra retakes control of the Empire and spreads his influence over the rest of Equestria. The Great Crystal War occurs. (The Cutie Re-Mark - Part 1)
Twilight is sent to the Crystal Empire to help save it as part of a test by Princess Celestia, and her friends accompany her.
Twilight finds the Crystal Heart and sends Spike to deliver it. With the Crystal Heart in place, the Crystal Ponies use the "love and light within" them to defeat Sombra. Cadance is recognized as the "Crystal Princess". Spike becomes known as "Great and Honorable Spike the Brave and Glorious" in the Crystal Empire for his role.
Season three
In unspecified chronological order...
Babs Seed visits Ponyville and becomes a member of the Cutie Mark Crusaders. (One Bad Apple)
Trixie returns to Ponyville with the Alicorn Amulet and beats Twilight in a magic duel. With the help of her friends, Twilight tricks Trixie into relinquishing the Alicorn Amulet and saves Ponyville. (Magic Duel)
Princess Celestia has Discord released from his stone prison on the terms of being reformed, a feat which Fluttershy accomplishes. (Keep Calm and Flutter On)
Plunderseed vines planted by Discord long ago emerge from the Everfree Forest and begin invading Equestria, capturing Princess Celestia and Princess Luna.
Twilight and her friends return the Elements of Harmony to the Tree of Harmony and destroy the plunderseeds.
Maud Pie leaves on her rocktorate dissertation. During this time, she finds Starlight Glimmer in the middle of constructing a village in which everyone is made to be "equal". (Maud Pie, Rock Solid Friendship)
Applejack obtains her key to the Chest of Harmony. (Leap of Faith)
Twilight Sparkle obtains her key to the Chest of Harmony.
Twilight and her friends unlock the Chest of Harmony and obtain Rainbow Power. With this power, they defeat Lord Tirek and imprison him in Tartarus again.
The Cutie Map summons Applejack and Rarity to Manehattan. Apple Bloom and Big McIntosh compete in the Sisterhooves Social. (Made in Manehattan/Brotherhooves Social)
Starlight Glimmer's old village holds its annual Sunset Festival.
The Mane Six, the princesses of Equestria, Shining Armor, and Flurry Heart are captured and replaced by changelings. Starlight Glimmer, Trixie, Thorax, and Discord come together to rescue them.
Starlight, Trixie, Thorax, and Discord infiltrate the Changeling Kingdom.
Through Starlight Glimmer's leadership, Thorax transforms into a new form of changeling, and the other changelings learn to share the love inside them.
The changelings are reformed, Queen Chrysalis' throne is destroyed, Chrysalis escapes, and Thorax becomes the new leader of the changelings.
Starlight Glimmer and her friends attend the Sunset Festival.
The students of Canterlot High School take a trip to Camp Everfree.
Sunset Shimmer, Twilight Sparkle, and their friends develop new magical powers.
The Mane Seven defeat Gloriosa Daisy when her overzealous desire to save the camp from closing leads to her transforming into a monster.
The campers organize a Crystal Gala fundraiser to raise money to save the camp.
Equestria Girls specials
The Rainbooms and Shadowbolts collaborate on a dance music video to win the Canterlot Mall Chance to Prance music video contest. (Dance Magic)
The Mane Seven are invited onto the set of the Daring Do movie and solve a prop theft mystery committed by Juniper Montage. (Movie Magic)
Starlight Glimmer travels from Equestria to the human world and helps stop Juniper Montage when she is corrupted by a magical hand mirror. (Mirror Magic)
Season seven
Starlight Glimmer, Trixie, Thorax, and Discord are awarded Pink Hearts of Courage, and Starlight graduates from being Twilight's student. (Celestial Advice)
In unspecified order...
The Mane Six go on a friendship retreat in Manehattan. (All Bottled Up)
Maud Pie graduates from the Equestrian Institute of Rockology and moves to Ponyville. (Rock Solid Friendship)
Spike goes through a molting phase and grows a pair of wings. (Molt Down)
Cozy Glow enrolls at the School of Friendship. Apple Bloom, Sweetie Belle, and Scootaloo receive honorary School of Friendship diplomas and are appointed as friendship tutors. (Marks for Effort)
Queen Chrysalis creates clones of the Mane Six in order to control the Elements of Harmony, but the Tree of Harmony destroys the clones. (The Mean 6)
Starlight is appointed as temporary headmare at the School of Friendship. (A Matter of Principals)
Gallus pulls a prank at the School of Friendship during Hearth's Warming Eve. (The Hearth's Warming Club)
Flim and Flam establish Friendship University with Chancellor Neighsay's approval. (Friendship University)
Starlight and Trixie take a road trip to Saddle Arabia. (Road to Friendship)
Scootaloo briefly joins the Washouts. (The Washouts)
Cozy Glow enacts a plan to remove all magic from Equestria, making use of several artifacts entrusted to Twilight by Princess Celestia.
The Mane Six and Spike travel to Tartarus to investigate Tirek's involvement in the disappearance of magic and learn about his alliance with Cozy Glow.
Cozy Glow imprisons Starlight Glimmer, and later Chancellor Neighsay, to enable her takeover of the School of Friendship.
The Mane Six and Spike escape from Tartarus, and the Tree of Harmony helps the Young Six thwart Cozy Glow's plans and restore Equestria's magic.
Cozy Glow is apprehended by the Canterlot royal guards and imprisoned in Tartarus.