2 years have gone by since the incident with Darth Maglus and Nyx is now officially adopted by Thomas and Twilight. And so everyone is heading to Canterlot to celebrate Christmas, but Shining Armor isn't too comfy around Nyx yet. But things may taker a turn for the worst when four droids from Darth Maglus' army are after Nyx and they hire a pirate named, "Sailor John" to help them. Now Thomas, Twilight, and their friends will need more help to stop them or it won't be a very merry Christmas. But there's another threat for them, Dragons.
Opening sequence/Dragon attack!
It has been 2 years since the incident with Darth Maglus and Nyx is now officially adopted by Thomas and Twilight. And is now the older sibling of 2-year-old Thomlight Sparkle, and Skyla, Yuna, and Sharon are learning to talk. And then suddenly, dragons start attacking! And So then the Equines and engines then prepare for battle. And soon they manage to hold them off. And soon after grabbing net full of sheep, the dragons leave.
Heading to Canterlot/The Remaining Droids
Soon, our heroes are on their way to Canterlot to go celebrate Christmas with their families. Although, Nyx isn't so sure that Shining Armor is still willing to trust her. She then decided to take her mind off it by reading a guide book to Dragons, but was surprised to find one page partly blank, involving a dragon called a, "Night Fury." Meanwhile, four droids that were in the Sith incident were contacting someone.
Arriving in Canterlot/Meet the Magic School Bus Gang
Soon our heroes arrived in Canterlot. And as they made their way to the Sparkle's place, they meet up with some old friends, the Magic School Bus gang! They then reveal they're old friends with the CMC. As well as Blythe, sees her school friends. And they introduce themselves to Nyx. Nyx is a little shy at first but starts laughing after Carlos says one of his jokes. They then soon arrive at the Sparkle's place and turn in for the night.
Meet Sailor John/Enter Spud the Scarecrow
Meanwhile, a Sailor is looking through a telescope from onboard a small dingy just outside Canterlot port. Then as our heroes are heading to pick up a Christmas tree, Thomas sets off to help Percy with the mail run for the night. And then they heard a sound. Our heroes look around nervously. Then out from a bush, was a scarecrow! Pepper then recognizes him to be Spud the scarecrow, her old friend from when she was younger. In a flashback, we see a younger Pepper sad, then sees a scarecrow. The Scarecrow then comes to life and begins dancing around. And then starts telling Jokes and doing funny things and makes Pepper laugh. And they become friends as the flashback ends. Spud then notices Nyx. And he makes funny jokes. Which makes her laugh and then they set off. Back with Thomas, he's chuffing along. And then he sees something rolling on the tracks. He then knew it was a boat! Thomas then sees a pirate! The Pirate notices him and introduces himself as "Sailor John". And then introduces Skiff. And he explains that he is in Canterlot for the holidays. Thomas decides to give them a push there. And soon they arrive in the town square but are seen by Blackie. After Thomas finishes with the mail job and meets back with the others, Blackie then sees John and Skiff. He then talks to John and asks what he's doing in Canterlot.
John explains that he and Skiff are just travelers. Blackie accepts but his seventh sense says otherwise.
Finding a perfect Christmas Tree/At the droids' lair
Soon our heroes arrive at a huge tree lot to find a tree and then they found a perfect one. However, it was too big. Then they found another but it was too small. Then another, but it was too wide and didn't have enough branches. But soon they find one that is perfect for the party. Meanwhile, the droids are at a lair and are building robot Sith Troopers. And they gave them a test tryout. When they test it out, they were successful.
The first strike
Then soon as our heroes make for the castle to deliver the tree. But as they do so they saw something, as some of them take a closer look, a blaster fires! And then the Sith Troopers emerge with electro staffs. Nyx deploys her lightsaber and duels them and cuts one. Showing they're robots! Then Sailor John appears and draws fire at the the robot troopers as they fire. And after a short battle, the robots retreat. And Nyx looks at them. And finds something else, a Sith coding!
Soon, they arrive at the castle and offer John to have him help with setting up the party, but he declines, saying he has to attend to other business, raising a suspicion from Blackie.
John meets up with the droids
Later, Sailor John up with the droids. And is cruel to them, blaming them to attack sooner than expected. They then apologized. Sailor John then states that their master is gone, and that. He then tells them not to attack until the real time comes.
Setting up the party/second strike/Accusations
Soon the party is getting set up. However, 3 of the droids from before sneak inside, they spotted Nyx. But decided to strike at her when she was alone. Afterwards, Nyx was helping to set up a candy cane lane, and was working on the upper deck on her own. And didn't know what was going to happen. Blackie was helping to lift one of snowflakes when he saw something. It was Twilight walking up (the droid pretending as her] but Blackie force push her, and she transforms to the droid and he activated his lightsaber. He then slowly approached the droid but the droid activated 2 red assassin lightsabers. And they dueled, as Nyx watches worriedly. But she failed to notice 2 other assassins approaching her from the rear. As Blackie continued to duel, he then noticed the other droids and then cut off the left leg of the droid he was dueling as he Force jumped onto the upper deck and pursued the other droids. But the deck way couldn't support the weight and began to give way. [slowly the deck began to break loose! Blackie then grabbed Nyx and jumped clear as the walkway and the Candy cane lane collapsed as everyone scrambled out of the way at the last second.
Later, the royal guards were called in as some of the team began to clear the wreckage. As Fluttershy calmed Nyx down, Blackie explained about the droids to Luna. While Shining Armor was checking over Cadance and others to make sure if they weren't hurt. And then he began to believe it was Nyx who made the candy cane lane collapse. But the surviving droids grab their wounded leader and leave. And Shining Armor began to claimed that Nyx was making it so the Sith could attack easier, but Jasmine slaps him and Twilight then argued with him about it.
Where's Nyx?!/Searching for Nyx/Kidnapped!
But when they stopped arguing, Nyx was gone! Nyx was alone, all in the cold. As she raced through Canterlot streets. Feeling very hurt after hearing Shining Armor claim that she was with the Sith. But then the 3 droids appear and claim they'll help her. She then races away and manages to temporally escape from them. meanwhile, everyone has formed a search party to find Nyx as Thomas went on his own, calling for Nyx. Shining Armor was still thinking that Nyx was just gonna lead the Sith to attack, then finally, Blackie lost patience and he sets out with Spongebob, Patrick, and Squidward to find her.
Back with Nyx, she slowly trudged through the snow, feeling cold and hurt. Then Sailor John appeared and asks why Nyx is all alone. She then tells him about what Shining Armor said and about the droids that tried to kill her. John then feels sorry for her and he decided to try and take her home, and they go into an ally, but when Nyx isn't looking, John knocks her out!
The Chase/The droids reappear
When Nyx wakes up, she's shocked to find herself gagged and tied onto Skiff's mast! Sailor John then reveals his true colors, he's working with the droids! Then he starts to get Skiff moving so he can deliver Nyx to the droids, but Skiff now annoyed says that he doesn't want any more part in the droids' plan but Sailor John stamps on him and tells him to keep his mouth shut, but then Thomas appears and sees them. And starts perusing them. Meanwhile, Spongebob, Blackie, Patrick, and Squidward are still searching when they see Sailor John, Skiff, and Thomas race by. Spongebob and Blackie get chase on their Harley motorcycle while Squidward and Patrick head back for the castle to tell the others. After blasting around a corner, Thomas sees a huge pirate ship! Sailor John plans to use the ship as extra wind power speed as well as stealing it for himself. Skiff shouts 'too fast' as Sailor John releases the anchor as Thomas struggles to catch up while Spongebob and Blackie are slowly catching up.
Meanwhile Ryan is puffing through the streets also looking for Nyx when he suddenly spots the Pirate Ship and races backwards shouting Pirates which confuses the Magic School Bus Gang who are knew by, and then they hear Thomas' whistle. Thomas then shouts at them to help him stop John. They quickly push some carts onto the tracks, which get caught in the pirate ship's wheels slowing it down. Then a rope gets caught on Ryan's buffer, he then brakes hard until he hits the buffer and the 72 tonne Tank Engine causes the massive Pirate Ship to topple over. As Thomas race by, soon followed by Spongebob and Blackie. Who tell the TMSG to contact the others. As the chase continues on, Sailor John then starts throwing several objects such as a shovel and Skiff's anchor at Thomas trying to slow him down to no avail. Slowly, Spongebob and Blackie begin to get along side of Skiff. And then John pulls out a stick of dynamite! And attempts to throw at Thomas.
But then Blackie shoots John in the arm, causing him to throw the dynamite to the side. Then from over the hill several headlights are seen, it was Blythe's motor scooter, Button's dirtbike, Dusty Crophopper, Percy, and the others who are in pursuit of Sailor John too. Then Spongebob sees a bridge that crosses over Skiff's line and drives the motorcycle across it and then they jump from the bridge and land onto the tracks, and start catching up to Skiff. But Skiff gets diverted onto another track. The other try their best to catch up, while Spongebob and Blackie manage to keep up by just. Then from another spot, Spud riding a wagon appears and then he rides off a jump and hits John head on, knocking him out. But as Spud gets control of Skiff, a droid drone snatches Nyx! And then Skiff crashes into a pile of flour bags. While Spongebob and Blackie continue pursuing Nyx.
Destroying the Droid quartet/Making amends
Then soon, the drone takes Nyx to an old factory. Where droids are being constructed. Spongebob and Blackie manage to sneak inside and watch as Nyx is put onto the wall as a firing squad is formed. Blackie then activates the neon light, giving the others a chance to know where the droids are, then Dusty cuts a tunnel though a wooden door, a metal door, and brick wall, allowing everyone else to get inside and then the battle begins! As the battle commences, Blackie sneaks over to Nyx and cuts her loose with his butterfly knife, giving her a chance to join the battle. As the battle continues, Nyx then takes advantages. She then destroys most of the elite droids. And then goes to face the four main ones, and they activate their assassin lightsabers. And they duel in a ultimate battle. At first it seems like they'll win but Nyx soon gain the upper hand and she defeated them all with a powerful force repulse.
And then she sees something, a machine to bring back Malgus. Nyx then attempts to go to it, but is cornered from Sailor John (who somehow managed to wake up) with his own lightsaber. And he challenges her. In a ferocious duel. And reach a statement. He then asks Nyx he can make her life better all she has to do is, but refuses. Then Twilight steps in and duels John. But John gains an upper hand and cuts off Twi's tail and is about to kill her, when Nyx picks up Twi's pistol and shoots him in the legs, and then Force pushes him over the side and is killed in the fall. Nyx then looks over and shuts down the machine. And then she falls to her hooves and cries, (not because of being scared, or because she's hurt, because she's happy to finally stopped the Sith that tried to take her away) as Twilight comforts her. Our heroes then head back for Canterlot castle, and when they return, Shining Armor looks at Nyx. And he starts to feel very bad for what he said earlier and apologizes for his actions. Nyx forgives him, however Cadance is still angry at him for making such foolish remarks. And refuses to talk to him. So then everyone turns in for the night, so they can be prepared for the Christmas party.
A Very Merry Christmas!
Later, they all wake up and head for the castle for the Christmas party, and they even have Skiff join in. Although, Cadance still isn't talking to Shining Armor. But after Blackie talks to them, they make up. And Spud begins singing "Holly Jolly, Christmas".
Second Dragon attack
Several days later, Nyx smells smoke. It turned out to be more dragons! The engines and equines then race out and start to fight them. But then a Monstrous Nightmare appears behind Nyx and attempts to eat her. And chases her, then Shining Armor notices it. He then races out and pursues it, and just when it almost has Nyx, he then jumps in and fights it. And the Monstrous Nightmare retreats. And Nyx thanks him. But then another Monstrous Nightmare appears but this time behind Snowdrop, but Primrose steps in front and tells Snowdrop to run. Snowdrop does so, but then the giant dragon kills Primrose! Afterwards a Zippleback and Flare Flyer head for Skyla. Nyx races for them but is surprised to see a dark blue dragon with green eyes fending Skyla. And it makes the Zippleback and Flare Flyer leave, it looks at Nyx for a moment and then leaves. But then a Fire Drake start heading for Sharon (who was sleeping not knowing what is about to happen). Then Celestia comes in, and to her surprise the dragon did not hurt Sharon at all. But then it saw Celestia with a firearm, and is about to blast her. When Barret jumped in and took the blast. The dragon leaves, and Barret tells Celestia to take care of Sharon and dies, and Celestia mourns for her husband. And Sharon cries.
Barret's funeral/The end
One day later, hundreds attended his funeral. And Sharon made her speech first. And explains how much he always love her father, and states she'll miss him. And Celestia states that they're all gonna miss him, very much. And buried his coffin as the film ends.
- This marks the first appearance of The Magic School Bus Gang, Sailor John, Skiff, Spud the Scarecrow, Ryan, Gator, The Maglus Droid Quartet, Dusty, and Ishani in The Chronicles of Equestria, and the Isle of Berk franchise
- The storyline concludes in The Beginning of the Chronicles III.
- Opening sequence/Dragon attack!
- Heading to Canterlot/The Remaining Droids
- Arriving in Canterlot/Meet the Magic School Bus Gang
- Meet Sailor John/Enter Spud the Scarecrow
- Finding a perfect Christmas Tree/At the droids' lair
- The first strike
- John meets up with the droids
- Setting up the party/second strike/Accusations
- Where's Nyx?!/Searching for Nyx/Kidnapped!
- The Chase/The droids reappear
- Destroying the Droid quartet/making amends
- A Very Merry Christmas!
- Second Dragon attack
- Barret's funeral/The end
- Star Wars Episode III: Revenge of the Sith - Palpatine's Seduction [when Sailor John visits the droids]
- Thomas and Friends: Sodor's Legend of the Lost Treasure: "Treasure chase" (when the chase happens)
- Holly Jolly Christmas - Spud the Scarecrow
- Star Wars Theme (for the end credits)