Following Team Shadow's defeat, Flash and his friends find themselves in Horizon City, a technologically advanced city where people and Pokémon use their bonds to live together peacefully and find new ways to help advance the world together. As a tournament is held in the city in preparation for the Equestria League taking place in just a few weeks, Flash finds himself experiencing a newfound fame for his role in defeating Sombra. But secretly inside the city, a young girl with dark dreams of power foolishly unleashes an ancient evil from Equestria's past, the Legendary Pokémon Centirek. Now with this uncontrollable evil free, Flash must work together with an unlikely ally to stop it before it destroys the world.
- 15 Minutes of Fame: This is discussed regarding Flash's new fame. Flash and his friends end up constantly getting swarmed by fans of Flash, due to his role in leading the battle against Sombra and dealing the final blow to him. Early on, Spike wonders if this is going to be a common thing from now on, and Doc notes that it is possible this is only temporary or it might become permanent depending on what Flash does next. Flash for his part at least never lets the fame he is getting go to his head, and agrees with Doc's statement that it depends on what he does next. Lightning Blitz however is very vocal about his disdain for Flash and his newfound fame and fully believes it won't last; though it is also pretty clear that he is jealous of Flash getting more attention than him.
- Beyond the Impossible: Centirek does this twice, with both of them being Played for Horror.
- Cozy Glow attempts to catch him in a Master Ball, a Poke Ball that is famous for being 100% guaranteed to catch any Pokémon without fail. But right when it seems like Cozy has successfully caught him, the Master Ball begins to crack and Centirek breaks out of it!
- All Pokémon in the series follow the four-moves limit rule from the games (that was eventually carried over to the anime). Centirek eventually breaks this rule when after having time to synchronize with the energy he stole from other Pokémon is able to use their moves himself, plus all of his own.
- Big Bad Wannabe: Cozy Glow is a young girl that plans to steal energy from other Pokémon so she can use it to revive the Legendary Pokémon Centirek, catch it in a Master Ball, and then use it to become the strongest trainer in the world, eventually planning to defeat Shining Armor, become the new champion, and later the Empress of Equestria. High ambitions perhaps, but her plans ultimately fail when things go horribly wrong when Centirek manages to resist getting caught in her Master Ball. So all she ended up doing was release an uncontrollable evil monster on the world, with no backup or contingency plans.
- Breaking Old Trends: This "movie" breaks a few of the patterns from the two previous ones in the series.
- The Legendary Pokémon introduced in this "movie" is not a good one needing help or protection, but an evil one that is the main source of the conflict.
- A human is not the Big Bad this time. Cozy Glow is initially setup as the main antagonist for the first half of the plot, but once she releases Centirek her entire plan falls apart and he quickly usurps her as the main antagonist.
- Starlight Glimmer is the main female character first introduced in this "film". But, unlike Sunset Shimmer and Sonata Dusk before her, she does not end up having any Ship Tease moments with Flash or end up falling in love with him. She actually seems to have some Ship Tease with Sunburst going on instead.
- Death Glare:
- Lightning Blitz constantly shoots Flash dirty glares whenever he sees fans rushing to meet him or praising him.
- Centirek gives one to Cozy Glow in response to her declaring that as the one who freed him he must now serve her.
- Enemy Mine:
- Once again, Alicormony and Dischaos join forces against a common enemy. This time they work together against Centirek again, but unfortunately can't finish the job.
- Flash and Springer team up with their arch-rivals Lightning and Gorillamp in order to stop Centirek's rampage.
- Famed In-Story: Flash is now highly idolized and recognized by many trainers due to his role in taking down Sombra and Team Shadow. He is practically a Celebrity Superhero, with fans rushing to meet him and requesting to have their photos taken with him or to have a Pokémon battle with him.
- Fusion Dance: The Poké-Arms System basically acts as this for a trainer and their Pokémon. It combines the two of them in the form of granting the trainer a Power Armor based on the Pokémon they combine with, granting the human all of the Pokémon's abilities and allowing the two to communicate.
- Heroic Bystander: Several trainers join Flash and his friends in the battle against Centirek. Unfortunately, all this really does is provide more Pokémon for Centirek to drain and become even stronger.
- Ignored Epiphany: Lightning Blitz works with Flash to help him defeat Centirek and save everyone, relying on Flash to deliver the final blow to Centirek while he holds him off for him. But, the final scene shows that Lightning hasn't learned anything from the experience, still dismissing Flash as a "worthless loser and a weakling that had to ask for help".
- "The Reason You Suck" Speech: When Twilight confronts Lightning over all the dirty looks he has been giving Flash lately, Lightning goes on a rant about how he still believes Flash is a loser who doesn't deserve any of this fame because he had to ask for help to beat Sombra, believing he could have beaten Sombra all by himself if he had the chance, and declares that once he wins the Equestria League, nobody will even remember Flash's name. Twilight quickly turns it around on Lightning by saying that Flash is already remembered better than Lightning ever will be, regardless of who wins the Equestria League.Twilight: That's why you didn't finish Sombra. All you care about is winning, and that's all you focus on. But Flash doesn't care about winning, and is willing to put other things he sees as more important ahead of what he wants. If he was given a choice between beating someone and helping them grow stronger, then he'll pick helping them. That's why people gravitate toward him. It's why Shining trusted him with ending Sombra.
Lightning: Right... Keep telling yourself that. It'll mean nothing when the Equestria League comes around. I'll crush him again without trying and then your brother will be next. So tell your friend to enjoy his fifteen minutes of fame. Because when I'm done wiping him out, no one will ever remember his name again... well, except for the nobody that challenged and lost again to the strongest trainer that ever existed: Me.
Twilight: Maybe. Or maybe he'll be remembered better than you ever will. After all, this isn't the first time he's saved the day. He's Flash Sentry, the boy chosen by Pegasoar who saved the Legendaries Eclixie and Sirenity from psychopaths that wanted to use their powers for themselves, and who led the charge against Team Shadow in the final battle. Honestly, Flash has done so much for the region that it doesn't even matter if you beat him in the Equestria League. He'll always be a real hero.
Lightning: Him?! A real hero?!
Twilight: Why not? Real heroes aren't always the ones who land the finishing blow or get the flashiest victories. They're the ones that put everything on the line so that the final blow can be landed. That's what it takes to really be a true hero. - Red Herring: Starlight Glimmer is setup as one early on. A cloaked figure is stealing energy from Pokémon with an energy gun. When Sunburst investigates, he finds a lot of evidence pointing to his friend Starlight, including designs for a device that looks just like the one the cloaked figure was seen using. Starlight is even seen working on the device in one scene, smirking at her work. But when she is confronted over this evidence, she says her device is meant to restore a Pokémon's energy, not steal it, and demonstrates by using it to heal a Lilligant. They quickly realize that Cozy Glow is the one behind everything, having stolen Starlight's pass-code beforehand and was the one stealing energy to awaken Centirek so she can capture him in a Master Ball and use him to conquer Equestria.
- Running Gag: Crowds of fans constantly recognize Flash and rush to meet him, with it often including Lightning Blitz glaring at this happening before storming off.
- Ship Tease:
- There are more instances with Flash and Twilight here. Early on in the story, a girl that's a fan of Flash's asks for her picture with him and latches on to his arm with a hug when he agrees, with Twilight crossing her arms and glaring at the display. Later, she practically sings his accomplishments to Lightning Blitz while saying he is already remembered better than Lightning will ever be.
- There is a bit of this between Starlight and Sunburst, with both of them being close friends and Sunburst being in disbelief when evidence suggests that Starlight is the one stealing energy from Pokémon.
- Tournament Arc: Subverted; Flash tries to sign up for the Horizon Cup after learning about it, only to find out the last slot was already filled. The tournament is never the main focus of the story, with only a few brief glimpses of a few of Lightning's matches seen occasionally, and never a full battle. After the final battle against Centirek, Lightning ends up winning the tournament, but it is given little to no focus and basically nobody cares, not even Lightning himself.
- Worf Had the Flu: Alicormony and Dischaos are defeated by Centirek and he absorbs their energy for himself, despite both of them having beaten him in the past. It is explained that they have had very little time to recover from the event with Sombra, and thus are both still weakened.
