Before it all begin, before Brian came to Equestria, before Yuna and her friends discovered Berk, before the dragon start attacking Equestria, there was a Sith Lord. He was determined to create their own Sith equine, however the ritual went wrong and their equine came out as a young foal, rather than a grown mare. Then, she escaped and landed on Earth (but got stuck in a thorn bush) and is taken care of by Twilight and Thomas the Tank Engine (who name her Nyx). And soon is start being disliked by others, but with help from a few of her new friends, she gains some of their trust. However, the Sith had arrived to bring her back and it's up to Nyx to save her new home.
Opening crawl/The Sith's ritual
In space, a group of Sith are creating something. Then the Sith lord "Darth Malgus". then comes in and exams it. He then asks when it will be made. The others then fired a beam for the creation. The beam fires. Then after a while he checks it out. But when he takes a look, it was a foal! Rather then a grown mare. Then the foal dangerously unleashed her powers to flee. She then race away as the droids try to stun her, but gets in a escape pod. And it flies away.
In Equestria/Snowdrop bullied
Down on Earth in the kingdom of Equestria, it's home of the ponies. But among them are also engines, steam and diesel. Standard and narrow gauge. And a host of others. At a schoolhouse, are young fillies and colts, but there's one who is an outcast and the new student, a blue and white pegasus, named Snowdrop. Who is blind. But 3 foals without any cutie marks; Apple Bloom, Sweetie Belle, and Scootaloo took her under there wing. And help defend her from the school bullies (2 earth ponies who are rich) Diamond Tiara and Silver Spoon. With help from Sweetie Belle's coltfriend (an earth pony without a cutie mark) Button Mash, and Apple Bloom's cousin; Babs Seed, as well as their friends; Blythe Baxter, Zoe Trent a singing, drama queen spaniel, Gail Trent, Zoe's younger sister, Pepper Clark, a comedian skunk, Mitzi, a beauty skunk, Vinnie, a lizard that loves to dance but he isn't very smart, Minka Mark, an abstract artist monkey, Sunil, a very skittish magician, Penny Ling, a ribbon dancing panda, and Russell, a hedgehog and the most serious pet, Vanellope von Schweetz, Joy, Aranea, Nellie, Barney, Pablo, Tyrone, Uniqua, Tasha, and Austin. And Snowdrop introduces herself to them. Then later they meet up with some more of their friends, narrow gauge engines: Skarloey, Rheneas, Sir Handel, Peter Sam, Rusty, Duncan, Luke, Mightymac (a double ended narrow gauge engine), Duke, Smudger, Bertram, Freddie, and Proteus (a magical narrow gauge engine). And the rest of their railway. While at a big building known as the Steamworks, works a cuban narrow gauge, named Victor and a clumsy crane known as Kevin. As well as Zecora, a herbalist zebra and Victor's spouse. (in which she is 3 months pregnant). Then we then see a blue tank engine with 2 coaches puffing on his branch line named "Thomas" and then meets up with his best friend "Percy".(another tank and a Canterlot Mail Engine) Then later he arrives at a huge oak tree, and meets up with a purple unicorn, "Twilight Sparkle." and her friends. (Applejack, Rarity, Fluttershy, Rainbow Dash, and Pinkie Pie) and Spike. (Twilight's little dragon assistant). Then later they are visit by some regal alicorns (Princess Celestia and Princess Luna). They share that their father, (King Solar Flare) spotted a Sith Escape pod come crashing down to Earth last night. And it looked like it fell into the Everfree forest.
In the Everfree Forest/Twilight's discovery
The group then search everywhere for anything out of the ordinary but find nothing, then Twilight falls into ditch. Then they find the ditch leads the wreaked pod.But after taking a look they find nothing. But the guards take the pod away for further investigation. Later that day, Twilight finds her saddlebags aren't anywhere to be seen! She then uses a locating spell and finds them in the ditch where the she fall in. Then thunder cracks and she gets nervous. But then she hears a whimpering sound. She then looks around and founds it coming from a thorn bush. Frighten and scared, she approaches the bush, not sure what is it, but inside she finds a black alicorn filly. But what really surprises her are the foal's eyes. They're dragon-like blue ones. That look like Nightmare Moon's eyes. She isn't sure what to do at first but she decides to help her, she then helps her get out of the bush and then thunder cracks again and the foal gets scared. Twilight then takes the foal back to the library as it begins to rain. When she arrives, she asks Spike to make something to eat as she heads into the bathroom to wash herself and to tend the foal's injuries. As she leaves the foal to rest, she goes to tell Thomas and Spike about her discovery. And are shocked about it. While Thomas is taking it calmly, Spike on the other hand is convinced she's a Sith, but Twilight assures him that she isn't and bribes him with a sapphire to keep quiet.
A disguise for Nyx
Soon, a few days past and Thomas and Twilight name the foal, "Nyx". But soon Twilight figures it might be time to take Nyx outside, but Thomas tells her that they should get her a disguise, so the others won't get suspicious. So Twilight heads for the Carousal Boutique. And then asks Rarity to make some causal wear. But when Rarity sees Nyx, she's at first not so okay, but after some reassuring from Twilight, she agrees to help. She then makes Nyx a purple vest, a teal headband and then Twilight adds some enchanted Glasses that can make Nyx's eyes look like a normal ponies' eyes.
Introducing Nyx/First day of school
Soon, after the disguise is complete, Twilight decides to introduce her to some of the others. Starting with her friends, then the engines. Then the next day Twilight has Nyx go to school. Nyx at first doesn't like it but later she begins to like it. However, she asks one question that has the class stay in a little longer before recess. Outside, Diamond Tiara and Silver Spoon start talking to her rudely. And then throw insults, when Diamond Tiara is shoved into a mud puddle, and it was Snowdrop! Snowdrop stands up for Nyx and then knocks Silver Spoon's glasses off and makes friends with Nyx. She then introduces her to the crusaders. After school was over, the 2 played and have fun. When Twilight arrived, she is surprised Nyx has a friend already. But then is proud to find that she has also made friends with the Crusaders. And the crusaders have made her a member of their club. Then Cheerliee gives her a note saying that Nyx will need some catching up on some subjects.
Nyx meets Jasmine
Then Nyx visits Canterlot gardens (along with Twilight) and inside the gardens, she meets up with Jasmine. At first she feels shy but soon, got use to her. And they introduced themselves and quickly made friends. And later, she meets the other princesses. And Princess Celestia and her husband, Barret Barricade show them their daughter Sharon (who was sleeping in a crib with a sound barrier glass [a glass that can't hear the loudest noise]). Then she meets Hiro, (Luna's spouse) and their daughter, Yuna. And then Princess Luna arrived. She introduces herself to Nyx. Then she meets Cadance and Shining Armor. And then they're own daughter, Skyla. And Twilight explains she's an aunt, Nyx is happy but later gets confused as they come into another room where they see Percy with a mail train. And Pinkie is helping to load the mail bags.
The Sith's plan
Meanwhile, back in space, Malgus tells his master that they lost the foal. His master is surprised and angry by his apprentice's failure. he then orders him to find it or else.
Sleepover at LPS/Nyx shows her wings
That night, Nyx was joining the Crusaders, Button, and Snowdrop in a sleepover at the Littlest Pet Shop. During a game of "Truth or Dare" Nyx is dared by Penny Ling to tell a secret she's never told anyone else. Nyx then takes off her vest and reveals her wings to them. Nyx expects the others to dislike her, but instead they loved her wings. Russell was most impressed, especially her wings. Because there were only a few known alicorns, but this was the youngest. he'd ever seen. After some more games they turn in for the night. But unknown to them, a droid was watching them and he raced away.
Telling Percy/Droid snipers
Then at the Canterlot Mail Station, Thomas is helping with the mail runs and then Percy notices him in deep thought and asks what's up. Thomas decides that he can't keep Nyx's possibly origin a secret from his best friend and tells Percy about where Twilight found Nyx. Percy was amazed but at the same time a little worried for Nyx, then there was gunfire! The Royal Guards then burst in and there were snipers. The Guards then fire back. And after a short fire fight, they check it out. They find the droids remains. They then report this the royals, who order them to keep an eye for anymore droids, as Thomas races back for the library and tells Twilight everything. She then starts get very worried about Nyx.
Last day of school/Celestia's visit/"Good Bye, Nyx"
Soon, on the last day of school. The foals race out excited, and Nyx goes to find her friends. At the same time, Thomas is returning from his branchline duties, but is shocked to find Princess Celestia's royal chariot at Farquarr. Then as he pulls in, Princess Celestia walks out and explains that Nyx is involved with the droid attack last night. Then, as Twilight and Nyx come into the scene, Celestia ask Twilight to come into the other room with her and Thomas while Nyx stays in the other. Soon, after her brief talk over Celestia then adds that she'll need to take Nyx back to Canterlot for some examination. Thomas is partly upset but understands, Twilight on the other hand is shocked. She doesn't wanna have Nyx leave but, after some explaining from Celestia, she accepts. But they are at least okay to give a Nyx a quick goodbye before she's taken. Nyx doesn't wanna leave, but Thomas informs her that she will be brought back. Twilight and Nyx share a hug and then she and Celestia leave to Canterlot, while Twilight falls to the floor and weeps.
The Sith attacks!/Nyx taken to Maglus
But shortly after the arrival in Canterlot, several droids storm the castle! As the guards battle them one of them grabs Nyx! And then at the ship. As the droids leave, Celestia orders no attack till further notice. But she has the guards contact someone. Inside the ship, Malgus tortures Nyx. Nyx then begs mercy. Maglus then decides that he will train her to be her apprentice, but she must pass one test: destroy Twilight and at last be a Sith Lord. Nyx is shocked, and refuses. But does so when Malgus threatens Jasmine, he then gives her a lightsaber. Then Maglus leaves the room as Nyx thinks about it.
Battling the droids/Twilight and Jasmine vs. Maglus/Nyx vs. Maglus
Soon, back on Earth, the Sith returns. And the droids are released and they draw fire at them. Our heroes head out and battle the droid army, but there are too many of them. As the battle goes on, Nyx is watching everything through the window on her spot from the ship. She is bashing the door to get free, but isn't having much luck then she picks up the lightsaber and cuts herself out. Back to the droid battle, the others are loosing ground. Then Twilight races for the ship and tries to find her.
But then, Maglus appears behind her and deploys his lightsaber. And Twilight does the same. They clash their sabers. And later Jasmine joins in. They duel the Sith Lord together. But Malgus overpowers Twilight. And then he zaps the 2. Nyx then races in and is shocked to find what he is doing. Maglus then tells her to kill Twilight. Nyx then activates the lightsaber and lifts up to prepare to stab her, but she can't find the heart to do it. She then starts to duel Maglus then Twilight throws Nyx her own Lightsaber and Nyx continues to duel Maglus with her and Twilight's lightsaber. But Maglus destroys Nyx's first saber, leaving Nyx to duel with Twilight's lightsaber and then she soon starts to overpower him. And then she cuts off his hands. And then she kills him. And then all droids outside, shut down. As Twilight, Jasmine, and Nyx escape as the remaining super battle droids and Sith leave.
Back to normal
After the Sith drones leave, Nyx is wondering what will happen to her. But the Princesses inform that she will be enrolled in Jedi training. And then Twilight then requests to train her and to also adopt her. And Jasmine asks to be Nyx's godmother. The royals agree to it just as Yoda walks up. He then grants Nyx as a Padawan learner and then he points out that Nyx now has her cutie mark. As Twilight hugs Nyx. And the movies ends with "You're where I Belong.".
- Yuna, Skyla, and Sharon are baby foals, while Zecora is pregnant with Zenorita in this film
- The storyline continues in The Beginning of the Chronicles II.
- Opening crawl/The Sith's ritual
- In Equestria/Snowdrop bullied
- In the Everfree Forest/Twilight's discovery
- A disguise for Nyx
- Introducing Nyx/First day of school
- Nyx meets Jasmine
- The Sith's plan
- Sleepover at LPS/Nyx shows her wings
- Telling Percy/Droid snipers
- Last day of school/Celestia's visit/"Good Bye, Nyx"
- The Sith attacks!/Nyx taken to Maglus
- Battling the droids/Twilight and Jasmine vs. Maglus/Nyx vs. Maglus
- Back to normal
- Music score: Jurassic Park III - Frenzy Fuselage [when Nyx escapes]
- Music Score: Sulley scares Boo (when Nyx is taken to Canterlot)
- [when the droids attack]
- Qui-Gon's Noble End (during Maglus and Nyx's duel)
- Trisha Yearwood - You're Where I Belong [end credit song]