Flash. Twilight, Doc, and Spike find themselves pulled into a Legendary adventure by a chance encounter. After pulling out a young girl, Sunset Shimmer, from a river, they learn she is on the run from a group led by the evil scientist Doctor Mechano, trying to protect the Legendary Pokémon Eclixie. Sunset was chosen by Eclixie to be its guardian and protector, so once it hatches from its egg she must help it get to the Eclipse Temple so it can get back home. But Mechano wants to use Eclixie to power his own wicked inventions, even if it means Eclixie will be stuck in their world forever. Can Flash and his friends help Sunset protect this Legendary Pokémon and get it home?
- Bittersweet Ending: It's sad to see Eclixie part ways with Sunset and the group, but Eclixie assures her guardian that she is special and shares a last bear hug with her. At the end of her journey, Sunset sheds tears of happiness, content that her mission is complete and that she can part ways amicably with Flash's group.
- Enemy Mine: Both Alicormony and Dischaos combine their powers to destroy Mechano's mech.
- Forceful Kiss: Before departing from the main group, Sunset plants a surprise kiss on Flash. Upon witnessing this, everyone is left dumbfounded, while Twilight quietly grumbles as Sunset's train leaves.
- Good Is Not Soft: Flash, Twilight, Doc, and Spike might have been willing to go out of their way to help Sunset when she was a complete stranger to them, but when she acts very secretive and protective of her bag and they end up getting attacked by Mechano's goons due to being near her, they quickly run out of patience and interrogate her over what is going on, throwing her in a seat and demanding answers.
- Mad Scientist: Mechano seeks to use Eclixie as a living battery to create portals to Alicormony and Dischaos, planning to drain their energy and become all-powerful.
- Mysterious Protector: The three equine Legendary Pokémon are this for the heroes throughout the story. They secretly assist them from the shadows several times without ever revealing themselves to them.
- Mythology Gag: The first Pokémon battle between Flash and the other trainer is a reference to the same battle seen in the opening theme sequence for Pokémon: The First Movie.
- Parental Substitute: When Eclixie hatches from its egg, Sunset promises to protect and take care of it, becoming a surrogate mother to it.
- Powered by a Forsaken Child: Mechano wants to use Eclixie as a battery, using its ability to open portals to pull Alicormony and Dischaos from their dimensions and drain their powers as well.
- Quirky Miniboss Squad: Forest, Pyron, and Cecelia act as Mechano's elite enforcers, spending a majority of the story hunting down Sunset and attacking her and the gang to try to steal Eclixie. They stand out as each having a fully evolved Equestria Starter Pokémon.
- Shout-Out: Forest comments "Alright, I've run out of patience." while chasing Sunset in the beginning.
- Suddenly Speaking: Zig-Zagged. While Eclixie doesn't speak proper words per se, it does suddenly communicate telepathically with Sunset when the two are about to part ways.
- Ungrateful Bastard: After the group goes out of their way to pull Sunset out of the river and get her medical attention, once she regains consciousness all she is concerned about is her bag and Eclixie's egg. When she sees Twilight has it she accuses her of stealing it and tries to snatch it back, with Flash needing to physically restrain her. They call her out on her ungratefulness, saying how they saved her.
- Villain: Exit, Stage Left: Forest decides to cut and run when he finds himself outnumbered after Pyron and Cecelia are defeated. This makes him the only antagonist of the story to escape any punishment.
- What Happened to the Mouse?: Forest makes his escape during the final battle when he becomes outnumbered, and is never seen or mentioned again afterwards.
