Thomas is still confused of his place as a Prime. Afterwards, Stuingtion's Engines share to our heroes of how they encountered a super powerful Decepticon called Megatrain the leader of the Deceptitrains, superpowerful Decepticons. And how he built a machine that could bring his huge army back to life. Then Tirek returns seeking revenge and intending to start the machine up and use Megatrain's army of Deceptitrains for his own purpose. So Mako and Spencer volunteer to keep an eye on Tirek. While searching for him, Spencer is called upon some strange thing and makes a deal with it. While that's going on, Tirek encounter Ernie who teams up with him and claims to be his co-leader. And Tirek accepts it. Later Optimus assigns Thomas to protect the Matrix, Blue Ruby, and Black Pearl from Tirek and Ernie, after Mako learns of his plans. After finding some energy Tirek's powers and strength grows then he heads to Canterlot to get the Matrix but finds out that the Princesses don't have it and that only a Prime wields it. When he come to Optimus and found out that he didn't have the Matrix, he froze him into an ice statue. Then found out Thomas was now a Prime thanks to a flag and realized he had the Matrix. The Princesses and Brian raced to Thomas and warned him. But Tirek and Ernie had followed, Thomas battles Tirek and Ernie, due to him holding the magic gems he could fire beams of magic from his gatling guns. The 3 reached a stale mate so Tirek and Ernie demanded Thomas to give him the Matrix. Blue Ruby, and Black Pearl. And if he did, he'd let him live to be his own train. But being loyal to Optimus, Thomas denied and stated how he would keep to the Prime's code. In which Tirek blasted him, seemingly vaporizing him as our heroes watched in shock.
But then the ground starts to rumble and then a huge robot raises out of the ground and reveals to be Megatrain! Megatrain then walked up to Tirek and pointed his cannon at Tirek planning to kill him in which our heroes were confused. Megatrain then explained about how he resurrected Tirek so he could steal energy but Tirek betrayed him and stole Megatrain's arc [which gave Tirek his ability to steal magic] then he put Megatrain in the prison of the Deceptitrains. And when Tirek blasted Thomas, he inadvertently activated a spell that brought Megatrain back, then he took his fusion, plasma cannon and vaporized Tirek completely for betraying him in which Optimus was restored to his own true form. When Tirek was killed, Megatrain took back his Arc and got his energy back. Spencer then revealed his deal with Megatrain and they flew for the machine, but after our heroes tried to convince Spencer to stop, Megatrain betrayed Spencer and he's no longer use to him and left him speechless. Spencer then released his mistake and raced to tell our heroes where the machine was.
Back at the scene of the battle Twilight was crying in Princess Celestia's arms of losing Thomas. Then Ernie walks up and Brian fights him, but then Sylveon bravely fight Ernie herself usingher Lightsabers aswell as Brian and Twilight's and manages to cut off one of his hands and then sends him falling off a cliff to his death. After Spencer pulled up, SpongeBob found Thomas perfectly unharmed. The Matrix, Blue Ruby, and Black Pearl had made a force-field over him. Then the other Trains-Primes temporally showed up and told Thomas that being the last Train-Prime was his destiny. Then the Matrix, Blue Ruby, and Black Pearl's power fused into one and turn Thomas and his friends into Trainbots, then they combined into a huge robot OpThomas Prime Supreme and flew for Megatrain. Once Megatrain started up his machine OpThomas Prime Supreme had flew up and destroyed the machine, then had a huge battle with Megatrain and killed him. After Megatrain was defeated, OpThomas Prime Supreme then returned each of the engines back to their old forms. After being grown by the Princesses, Twilight and Thomas shared a hug. Spencer then apologized for his deed as Optimus sent a message out of how Thomas become a true Prime.
- Tirek and Ernie will be the antagonists in the film until Megatrain kills Tirek in the end.
- This movie marks Megatrain's first appearance ever in the Pooh's Adventures saga.
- Thomas and his friends become Transformers in the end.
- It's reveled that Tirek had betrayed Megatrain years ago.
- This movie's based off the My Little Pony: Friendship is Magic episodes: "Twilight's Kingdom parts 1 and 2".
- Confused about his place
- Stuingtion's engines tell the story of Megatrain
- Tirek's return
- Sending someone to spy on Tirek
- Spencer's deal with Megatrain
- Ernie teams up with Tirek
- Optimus assigns Thomas to protect the Matrix, Blue Ruby and Black Pearl
- Tirek's arrival at the Canterlot castle/Discovering the truth
- Warning Thomas
- Thomas, Tirek, and Ernie's battle
- Tirek's request/Thomas' sacrifice
- Megatrain rises!
- Megatrain's story/Megatrain kills Tirek and regain his Arc
- Spencer cappers the others
- Megatrain's betrayal to Spencer
- Spencer helps our heroes
- Thomas and his friends become Trainbots
- OpThomas Prime Supreme rises!
- Thomas' place found at last
Songs and soundtrack
- You'll Play Your Part - Princess Celestia, Luna, Cadance and Optimus
- Legend/Altomare (from Pokemon Heroes) (When Megatrain's backstory is told)
- Preliator [when Thomas, Ernie, and Tirek battle]
- Lord of the Rings: The Prophecy [When Megatrain rises]
- Simba vs Scar (when Sylveon duels Ernie)
- I Rise, you fall [when Megatrain dies]
- Transformers: Prime theme [playing during the end credits]