On Route 10, the wild Pokémon Team Flare kidnapped from the Pokémon Village cringe with unimaginable pain as their life force is slowly drained away by the stone pillars they are strapped against. The Santalune Gymleader Viola wastes no time to go airborne on her Vivillon, and tells Yvette to come along with the others. Yvette promptly commands her team of Sky Trainers to follow Viola's cue, and states that it is time to seek justice and redeem themselves as Vivillon specialists from the humiliation Team Flare caused them. Viola wants everyone to focus on freeing the Pokémon from the stone pillars, which she believes will instantly stop the process of bioenergy extraction.

Staying on ground level, Alexa urges her sister and the Sky Trainers to stay alert, and not to carelessly get imprisoned by the stone pillars themselves. She then joins Clemont and Bonnie, and together as the electric team, get ready to destroy the stone pillars as soon as the wild Pokémon are freed since it is the only surefire way to stop the Ultimate Weapon's activation. At that moment, Chalmers and the female Admin finally realize that Alexa's Helioptile and Clemont's Heliolisk have set up an Electric Terrain in the entire area, which allowed them to disable the sleep traps of the Amoongusses and even strike down the Venomoths that are supposed to guard the aerial route.

While the two Team Flare Admins find themselves rendered helpless by the team work of their intruders, Delphox stands its ground and attacks mercilessly. It whips up a Fire Spin with its branch to keep the Vivillons at bay, and follows by spitting out a Mystical Fire towards Clemont and Bonnie. Fortunately, the Lumiose Gymleader reacts in time and manages to duck sideways while lifting his sister off with his Aipom Arm before the attack makes contact. Seeing the tactful strategy employed the fire fox even without a trainer's guidance, Clemont is genuinely astonished by how powerful it is.

Up in the air, Viola comes up with a plan, and gets the Sky Trainers to have their Vivillons form a circle by using Hold Hands. The ring of varied-wing-pattern butterflies then begin to spin and simultaneously set up a combined Safeguard. Due to the centrifugal force, the move's protective effect quickly covers the entire area, and Yvette states that neither the land nor aerial teams have to worry about getting burnt anymore. On Viola's cue, the clustered Vivillons split up again and rapidly dive towards their rescue targets. Soon, the captured wild Pokémon from the Pokémon Village are picked off from the stone pillars one after the other despite Delphox's persistence in trying to fend off its intruders. Behind Delphox, Bonnie creeps her way to the emptied stone pillars, and begins to destroy them one by one with Dedenne's electric attacks.

Meanwhile, Chalmers gets hold of the male Grunt responsible for communication, and demands to know if there are any nearby troops they could summon. To his dismay, the Grunt reports that all troops have been dispatched to fight the Elite 4, and they have all of a sudden lost contact with the security teams stationed at Shalour and Cyllage City. Just then, the Grunt manages to establish connection to the Cyllage team, and Chalmers promptly snatches his headset away for himself. Speaking with a desperate tone, he explains that they are under massive attack, and calls for immediately assistance on Route 10. However, whoever is speaking on the other end replies with a garble of cryptic and meaningless expressions, and Chalmers demands to know what he is talking about. Soon enough, he discovers that the person he is conversing with is actually not a Team Flare Grunt but Wulfric, and the Snowbelle Gymleader informs him that his security team has already been crushed by the Gymleader team, who will gladly advance towards Route 10. Hearing that, Chalmers drops to his knees, and gets washed over by a sense of total despair. The female Admin wants to know what happened, and Chalmers, with a defeated tone, relents that perhaps time is up for Team Flare.

In the woods near Route 19, Tierno is having a hard time dealing with the Team Flare Scientist Mable. With Corphish badly scorched, Houndoom slams it to the ground and keeps its forefoot on its back while unleashing an Inferno at Tierno, which not only melts his Roller Skates but begins to burn his legs as well. Mable mocks that Tierno should really have given up before he got himself and his Pokémon in such battered states, but the big boy grunts that the battle isn't over yet. He points out that Corphish still has its pincers fastened around Houndoom's foreleg, which it will never let go no matter what. Indeed, despite being severely injured, Corphish keeps a strong grip on Houndoom, and Mable finds it annoyingly stubborn. Tierno grins that the stubbornness is shared between trainer and Pokémon, and says he has waited 5 whole years for his friend to emerge from his seclusion at home. At that moment, Corphish evolves into a Crawdaunt, and delivers a Guillotine, slamming Houndoom unconscious while knocking Mable over at the same time.

Nearby, Shauna is battling Celosia, the other Team Flare Scientist who has previously mind controlled her. Taking shelter behind a tree, Shauna keeps her guard on as Skitty gets into a close-up combat with Celosia's Doublade. The purple-haired Scientist finds it amusing that Skitty is neither dodging nor taking hits but is simply rolling itself against Doublade like a fur-ball. Shauna states that she has learnt a lot from training with Gurkinn, and Celosia applauds her efforts. However, she doubts that Shauna can really achieve anything in this battle, and starts to wonder if she should perhaps toy with Aegislash's illusions again. Hearing the word 'illusion', Shauna's horrible memories come flooding back immediately and she flinches a little. As she gets momentarily distracted, Skitty loses its pace and is struck away hard by Doublade.

With a laugh, Celosia states that while Shauna's skills may have improved with training, her mind remains weak. Shauna disagrees however, and says one works much harder after failing once. At that moment, Skitty bounces back to its feet, and Celosia is shocked to see that it has barely sustained any injuries. Shauna orders a Feint Attack, and the pink kitten promptly smacks its tail onto Doublade with a somersault, fainting the sword Pokémon with the super effective move. Celosia quickly checks on her unconscious Pokémon, and notices with astonishment that its blades have been wedged all over with Skitty's fur, making them blunt and effectively reducing their ability to inflict damage. Grunting with frustration, she realizes that Skitty wasn't just simply rolling around and has secretly used Play Rough to weaken Doublade.

Shauna thinks she will not deny the fact that she is a weak trainer, which is why she has asked for assistance and it is time for her help to show up. As soon as she says that, a humanoid Pokémon hops onto the battlefield, and Celosia gasps in bewilderment that it is Korrina's Lucario. Shauna says Lucario's aura safeguards her from illusions, and tells Celosia to quit tampering with her mind again. With that, she orders a Foresight followed by Aura Sphere from Lucario, which not only takes out Aegislash but also brings down Celosia, shattering her visor as it hits the floor. With her nemesis defeated, Shauna feels overwhelmed by relief and starts to get wobbly. Lucario quickly steadies her, and Shauna wishes that Gurkinn and Korrina are here to see that she has finally done it.

Just then, Tierno finds Shauna, and they are both glad that the other is alright. Shauna notices the burn on Tierno's leg, but Tierno tells her not to worry about it and suggests they go search for Trevor, who shouldn't be too far off.

Indeed, further south in the woods, Trevor is battling the green-haired Scientist Bryony. Earlier, Y's Croaky has trapped Bryony and her Bisharp with its Mat Block and frubbles, but a few slashes from Bisharp's blades are all it takes to set them free. Bryony spots Trevor hiding in a nearby bush, and orders Bisharp forward to attack. The sword blade Pokémon brutally slashes off the boy's head, but Bryony soon discovers that it is just a Substitute created with Greninja's frubbles. At that moment, Croaky and Trevor's Floette ambushes them from behind on a nearby tree branch, and sends out a Fairy Wind assisted Water Shuriken. The combo attack hits Bisharp and Bryony hard from behind, and takes them both out before Bryony could fully figure out what happened.

Letting out a sigh of relief, Trevor gets down from the tree he is hiding on with Croaky's help, and thanks the Greninja for its great work. However, a voice comes on to say it is too early to celebrate, and a Pumpkaboo instantly presses against his back menacingly. Trevor throws his arms up in fright, and Aliana shows up with a giggle, warning Croaky not to do something stupid or the real Trevor will be beheaded this time. Yet, before the orange-haired Scientist could do another giggle, a pair of pincers grips at the back of her collar, and she becomes the one being warned not to move. Clearly, Tierno and Shauna have arrived with their Pokémon, and it seems that the three Vaniville kids have emerged victorious in their battle against the Team Flare Scientists.

Back at the Pokémon Village, the intensive battle between X and Lysandre ensues. While Elec targets its electric attacks on Gyarados and Garma keeps Pyroar busy, Salame, Rute, Kanga and Li'l Kanga work together to combat the legendary Zygarde. Lysandre sees that X's Chesnaught Marisso is the only Pokémon guarding him, and commands Pyroar and Gyarados to turn their focus on the boy, since taking him out will effectively disable his Mega Pokémon. Y calls out to warn X about the incoming assaults, but to her astonishment, X seems completely oblivious to his surroundings and appears to be caught in some sort of a trance. Fortunately, before Pyroar and Gyarados close in, Green and Blaine arrive and strike them back with Charizard and Mega Mewtwo X.

Y feels glad that the two have regained consciousness, and Green tells X to keep his attention on Zygarde while they take care of the rest. However, X once again gives no response, and Cassius and Emma, who have caught up with the group, point out that the boy's behavior is rather strange. Blaine explains that Mega Evolution is the result of a trainer mentally bonding and linking with a Pokémon. Given that X is simultaneously bonding with 5 different Pokémon, it isn't hard to imagine the tremendous burden on his mind, which is why even without Green telling him , his awareness is currently only on Zygarde and nothing else. Indeed, in X's eyes, the Kalos Watcher is all he sees now, and his every thought is transfixed on defeating it.

As the battle goes on, Y notices that some mysterious substance seems to be detaching from Zygarde's body. Cassius agrees that he sees them too, and Emma points out that they appear to be the same materials Zygarde summoned and collected from its surroundings during their battle in Anistar. Y bolts that they are indeed the small green squishy blobs they saw before, and Emma recalls seeing Zygarde absorb a lot of them. She believes that it does so to strengthen itself, and its tremendous power is perhaps the result of the being the collective body of all these small squishy blobs. Hearing that, Y couldn't help but wonder if Zygarde is starting to break up because X's attacks are working, but Blaine suspects that it may also be due to the fact that it doesn't need this power anymore.

In the woods near Route 19, Trevor, Tierno and Shauna continue south towards the direction of the Pokémon Village but are soon met with an astonishing scene. Right in front of their eyes, Xerneas locks its antlers against Yveltal's neck, and the black bird fastens its claws around the blue deer's horns at the same time. It soon becomes apparent that neither creature is moving, almost as if they are frozen in time. Tierno notices that Xerxer's antlers have lost their rainbow hue and turned a pale shade of blue, and Yveltal's eyes have also become dead white. In that instant, the Vaniville kids begin to hear Xerneas telepathically, including X and Y who are far away from the site. Y, who has communicated with Xerxer through this manner before, immediately recognizes its voice, and X, despite still entranced by his task to defeat Zygarde, manages to hear Xerneas's every word loud and clear as well.

Xerneas explains to the kids that it has realized from its brief encounter with Zygarde that it is the Watcher of the ecosystem. When Xerneas clashed with Yveltal, their destructive forces threatened the ecosystem, which forced Zygarde to store up a huge amount of power to curb and overcome them. However, Zygarde itself doesn't really want these powers, nor does it wish to exercise them. That said, when it no longer has a task, Zygarde would have no need of its stored-up power anymore.

Trevor bolts at what Xerneas is implying, and at that moment, the legendary blue deer begins to turn into a tree while the dark bird folds itself up into a cocoon, intertwining with the tree's branches. Xerneas telepathically bids farewell to the Vaniville kids, and hopes that it has sown a seed inside every one of them. With that, the two legendary Pokémon fully revert to their dormant formes, and Zygarde senses this from a distance. Letting out a shriek, its body starts breaking up into even more small green blobs, and Emma thinks it is disintegrating. Y feels a tug at her heart that Xerxer has gone, and Lysandre doesn't understand what is going on. At that moment, X orders a Superpower from Rute, Dark Pulse from Garma, Thunder from Elec, Outrage from Kanga, and Flare Blitz from Salame, and the combined attacks cause Zygarde to break up even quicker.

Up in the air, Diantha continues her fight with Malva, and the fire expert takes pride in the fact that her Talonflame is much faster. However, she soon notices what is going on down below, and watches with horror as Zygarde explodes into a million green blobs. Her momentary distraction allows Gardevoir to land a hit on Talonflame, which throws Malva off from its grasp. Malva begins to plummet, and Diantha hurriedly hovers down to assist her. Yet, Malva slaps away the hand Diantha reached out for her, and dives towards Lysandre, who is tumbling down amid Zygarde's disintegrating body towards a ground of sharp broken boulders.

Lysandre and Malva's fall end with a loud thud, and everyone watches with uneasy expressions as the Team Flare Boss lies in a pool of blood while a motionless Malva lays sprawled on top of him. Lysandre wants to know why the Ultimate Weapon's beam of purification has yet to be fired, but Malva, who is soaked in her own blood, can no longer give him a response.

And so, it seems that the evil schemes of Team Flare have finally been put to rest. On Route 10, the wild Pokémon from the Pokémon Village rejoice at their regained freedom as the Gymleaders of Kalos gather with relief. Viola shakes hands with Yvette, and Shauna's Furfrou wears a look of sorrow as it steals a glance at the fallen Delphox. Back at the battle site, the three other members of the Elite 4 arrive, and Wikstrom picks Malva up into his arms while Drasna, Siebold and Diantha gather near, each harboring complex emotions towards this young woman who is supposedly a comrade but ends up being a foe.

As for the Vaniville kids, with their task at the Pokémon village complete, they begin their journey back to Lumiose City where Prof. Sycamore awaits. Cassius offers them a ride, and with the exception of X, everyone instantly falls asleep out of exhaustion upon getting on the van. In addition to finding peace that they can finally resume their ordinary life, they also feel a little proud of themselves that they have freed the Kalos region from peril and insecurities. Soon enough, Cassius's van arrives at the gate of Lumiose, and the kids wave goodbye to Cassius's group as they step into the city.

Alas, the scene in front of their eyes astonishes them.

Everywhere, people carry on with their daily routines as if nothing ever happened. Young lads and girls stroll down the streets in flamboyant outfits; old ladies groom their Furfrous and have luxurious afternoon teas in cafes; street musicians play their hearts out as tourists go on shopping sprees and snap photos everywhere they go. It's as if the threat of the Ultimate Weapon never occurred, and people are just enjoying life as they usually do.

Trembling with disbelief, Shauna doesn't understand what she is seeing, and recalls that the wild Pokémon on Route 19 behaved the same way after the crisis. Tierno tries to comfort her, and says these smiles on people's faces are what they have been trying to safeguard. However, a wealthy couple walks past the group at that moment, and sneers at their filthiness. They postulate the kids to be part of the Lumiose Gang, and hopes the city would rid of them someday. Tierno finds himself speechless at the couple's cruel words, but X on the other hand, seems not too surprised.

Lowering his gaze to the ground, X points out that if Vaniville wasn't the town Xerneas and Yveltal destroyed, and they weren't the ones ambushed by Team Flare, they will perhaps be among the people who smile and act as if nothing ever happened. The fact is, even for those who have sided with Team Flare and chosen to support Lysandre, now that the organization is dissolved, they would pretend that they were never involved and walk among them with no remorse of what they did or believed. Shauna finds the notion hard to accept, but Y shares X's sentiment, and states that in a sense, Team Flare is never truly dissolved. X and Y's words hit Trevor hard, and he starts to wonder if they can really resume their ordinary life and go back to being amongst these smiling people who act as if nothing ever happened.

At that moment, a voice comes on to ask how they plan to live on as Pokémon trainers in a Kalos like this, and the kids turn around to see AZ, the tall man whom they encountered previously at Team Flare's underground HQ in Geosenge Town…