High up in the air, Diantha orders a Charge Beam from Gardevoir, but Malva easily fends it off with Talonflame's Razor Wing. She mocks that Diantha probably still takes pride in being the Champion of Kalos, but such a title shall soon be made meaningless. With that, she commands an Acrobatics and Talonflame plunges itself into Gardevoir's back with its sharp beak, inflicting massive damage on the humanoid Pokémon. Diantha grunts in frustration as Gardevoir winces in pain, and Malva compliments Talonflame for its great work. She points out that the fire bird is currently showering ember between its feather gaps, a sign of it being in the fever of an exciting battle, which is exactly how she feels. Licking her lips, she savors the rush that she is getting from the combat, and wishes Lysandre can witness this scene with his very own eyes.

Meanwhile, Trevor hides behind a tree with his Floette, and is contemplating on how to deal with his pursuer, the Team Flare Scientist Bryony. Despite feeling empowered by Y's encouragement earlier, the orange-haired boy still couldn't help but panic in face of such a powerful foe. At that moment, he steps on a broken twig, and the sound catches the attention of Bisharp, who quickly lashes out with its blade-like arms. The attack easily cuts up the giant tree which Trevor is taking shelter behind, and Bisharp lunges forward with a follow-up strike. However, the shredded wooden planks suddenly close in on Bisharp and Bryony, and Bryony recognizes the move as Mat Block. Croaky soon shows itself and Trevor realizes with pleasant surprise that Y has left it behind to help him. Giving the Greninja a hug of gratitude, he once again finds his confidence and tries to recall the ninja frog's known attacks.

At the Santalune Gym, Viola is astonished to learn from her sister that the Ultimate Weapon was created 3000 years ago. Alexa shows her a record of tales that have been passed down verbally through generations, which described the weapon as 'an evil flower that takes away the life forces of humans and Pokémon'. Apparently, once the weapon is filled with adequate bioenergy, it would unleash a beam so terrible that it is beyond imagination. Viola wonders if there is a way to stop this weapon, and Alexa points out that if they count back from their current day, the ancient war ended exactly 3000 years ago. Violet catches the insecurity in Alexa's voice, and wants to know if something is bothering her. Alexa says she doesn't really know, but admits to be feeling unsettled for some unknown reason.

Back at the Pokémon Village, the clash between Zygarde and Mewtwo ensues while X is still having a hard time digesting what Emma just said. Lysandre orders a Dragon Pulse from Zygarde, and Emma quickly relays his command to the legendary Pokémon almost robotically. X tries to stop her but unfortunately to no avail. The powerful attack unleashed by Zygarde hits Blaine directly, and inflicts an equal amount of damage on Mega Mewtwo X due to their synchrony. The two lay motionless on the crumbled ground following the strike, and Lysandre grins that they are almost done with. Using his command device, Lysandre orders Emma to stand up, and the young girl does as she is told. X fervently attempts to stop her again, but Emma doesn't understand why, explaining that she is simply doing a job she is paid for, for the sake of Cassius.

Hearing that, X suddenly recalls what Emma said before while they were infiltrating Team Flare's base at Geosenge Town. He remembers her telling him that she likes Cassius a lot, that even though she was not able to give him any help on the Pokémon Storage System, he would never do anything terrible to her. X confesses to Emma that he too, used to be fearful of adults and strangers. Even for acquaintances, his trust in them may falter in a day's time. For this reason, he has shut himself away at home. With no goal and no dreams, he became devoid of any will to achieve anything. At that time, he genuinely felt that he was worthless, and remained in this state for 5 whole years.

It wasn't until Xerneas and Yveltal attacked Vaniville that he was forced to leave home against his will and go on a journey which he detested at the beginning. On their way, their group was repeatedly ambushed by Team Flare, and they couldn't even sleep at night without fearing that the enemy was just around the corner. It was at that point that he finally realized that he actually had everything. He had a home, a room to his own, food, and most importantly, friends and Pokémon. Everyone was waiting for him to come out of his shell, waiting for him to pick up where he left off before he went into seclusion.

Throughout his journey, he has met many different people and Pokémon, all of whom have had their lives turned upside down thanks to the deeds of Team Flare. However, despite that, they still helped their group and lent them their strength selflessly, even to the point of putting their own lives at stake. If he hadn't left his house, he would never have known that such people still exist in the world. He realizes that Emma has seen all kinds of cruelty and harshness from her early exposure to the outside world, but he also believes that there must be kind souls she has met whom she cares about. Speaking from his heart, he urges Emma not to betray the trust of the people and Pokémon whom she treasures, for such an act will pain them deeply.

At that moment, Lysandre raises the control device and commands another Land's Wrath from Zygarde. This time, however, Emma becomes hesitant in relaying the message, and holds her head in pain as she struggles with her thoughts. X asks if she is alright, and suddenly feels a tap on his shoulder. It turns out that Cassius has arrived with his Gourgeist, and the man believes that X's words have successfully gotten through to Emma. Lysandre, on the other hand, feels irritated that the girl isn't following his orders. He demands to know what she is doing, and Cassius mocks that he has never heard of a job where the employee will be mind-controlled to the point that it starts to corrupt her senses. He states that what Emma was tricked to sign up for is clearly more than just an ordinary job, and Lysandre makes no effort to hide the fact that the girl is nothing but his pawn. With an evil grin, he pushes her to attack again, and further adds to the stress on her mind.

Cassius lets out a sigh, and knows that he was part of the reason Emma went job hunting. He tells the girl that she needn't continue with this job anymore, and wants her to just come home. Hearing that, Lysandre barks that Emma's worth is only valid when she has the suit on, and her worthless existence can only redeemed by her reigning as Team Flare's Essentia in the beautiful Kalos that is about to be reborn. The man nudges onto the control device to demand another attack, and Cassius decides that he's had enough. He scoffs that he will never know how majestic it is to reign, but to take away other people's freedom and corrupt their lives is surely a shame. With that, he gestures to his Gourgeist, who fires a Shadow Ball to shatter the control device in Lysandre's hand.

With the device broken, Emma regains full control of herself, and gets Zygarde to aim its Land's Wrath on Lysandre. However, before she could finish her command, Mega Gyarados brutally picks her off the ground in its jaw and slams her back down, knocking off the Pokeball which she used to capture Zygarde. The Pokeball falls into Lysandre's hands, and the Team Flare Boss is elated that he finally has direct control of the Kalos Watcher. Wasting no time, he commands a Land's Wrath, and the ground beneath X, Cassius and Emma immediately explodes into a million pieces.

Up in the air on Fletchy, Y cries out in shock as the attack floors everyone on the ground. She quickly calls forward Solsol to attack, and activates her Keystone to Mega Evolve it. The Mega Absol instantly fastens its teeth on Lysandre's left hand, and causes the man to howl in pain. Pyroar rushes to its trainer's rescue, and lowers Solsol's attack with a Noble Roar before digging its fangs into the disaster Pokémon's neck. With a thrust of its head, it hauls Solsol away from Lysandre, but as it does so, the Mega Ring on Lysandre's finger is also torn off bloodily, which instantly causes Mega Gyarados to revert to its usual state. Fuming with rage, the Team Flare Boss couldn't believe that his Keystone is taken away, but Y retorts that he was the one who took it away from Korrina in the first place. Lysandre angrily commands a Hydro Pump from Gyarados, and the powerful attack not only faints Fletchy but also knocks Y down from the sky.

Just then, Lysandre receives a call from Chalmers, who reports that the bioenergy extraction process is set to begin. Lysandre finds it amusing that the report arrives just as all the worthless beings are taken care of, and thinks it must be heaven's will. He tells Chalmers to proceed with the extraction, and decides that it is time for him to make his final announcement.

Soon, Holo Casters across the region begin to broadcast a live message from Lysandre, and the man starts off by thanking the residents of Kalos for making his product a big hit, allowing his big announcement to get across the land so easily. He hopes that everyone is paying good attention, because Team Flare's purification of Kalos is about to begin, which will clean the land of all chaos and ugliness and return Kalos to its true beauty. For the chosen ones, he invites them to help him build a better Kalos. For those who are not, he must unfortunately say goodbye to them.

With that, the message cuts off, and panic starts to spread across the region. While some question if it is merely an advertisement for a new model of the Holo Caster, many more are frightened by what they heard personally from the inventor of the device. At the Santalune Gym, Viola and Alexa realize with horror that Team Flare must be trying to activate the Ultimate Weapon again, and they are soon approached by a group of unexpected guests.

Back at the Pokémon Village, Y, who has survived her fall thanks to Veevee, checks on X, and the boy frantically asks if Emma and Cassius are alright. Cassius shows himself with Emma on his back, and tells X not to worry as they managed to survive. Emma points out that Lysandre is heading off with Zygarde, and Marisso soon brings back a battered Blaine and Green, both having passed out from the intense battle. At that moment, something slips off from Green's hand, and X sees that it is the Mega Charm harboring Diantha's Keystone. Y takes out the Keystone of Korrina which she retrieved from Lysandre, and remarks that they suddenly have so many Keystones at hand. Seeing the Keystones, X ponders on how Mega Evolution only occurs once per Keystone per battle, and is suddenly hit by a radical. He begins to pull off the Mega Ring from Green's finger, and a startled Y asks what he is doing. X apologizes to Green for his rudeness and promises to return it afterwards, and tells Y to give him her Keystone along with Korrina's as he may have figured something out.

On Route 10, also known as the Menhir Trail, the wild Pokémon Team Flare kidnapped from the Pokémon Village struggle in agony as the stone pillars they are tied against start draining their bioenergy away. With their mouths wide open, they all wear looks of terror and despair as their life force is slowly sucked out of their bodies. Chalmers marvels at the power of the ancient Absorber but the female Admin finds herself feeling nauseated by the scene. Chalmers thinks it is understandable since the sight before them is quite gruesome after all. Surprisingly, Delphox remains unfazed and emotionless despite being a Pokémon itself, and one can tell that it has inherited the traits of Malva whom it was trained by.

A male Grunt walks up to the female Admin to report that surveillance of their surroundings is clear, and the female Admin isn't too surprised to hear that since they have troops of Amoongusses and Venomoths guarding both the ground and air. With their powerful Sleep Powder, any human or Pokémon that dare to come near would instantly be put to sleep. That said, she tells the Grunt not to let their guards down and watch out closely for unexpected intruders. Suddenly, Delphox senses something, and wears a frown as its stares at the floor.

Meanwhile, Lysandre is moving away from the Pokémon Village with Zygarde and is advancing towards Geosenge Town. Before he could venture too far, however, X and Y manage to catch up with him. Lysandre sees that X has called forth his entire team, and is surprised that he still hasn't given up. X thinks of all the people who have helped him on his journey, and begins to focus his mind on the 5 Keystones he currently possesses: Korrina's on his left middle finger; Diantha's around his neck; Green's on his right middle finger; Y's on his right wrist; and his own on his left wrist. Summoning their powers, he calls for their light to intertwine with those of the 5 Mega Stones, and in a blinding flash of seven-coloured light, Kanga, Elec, Garma, Rute and Salame all Mega Evolve simultaneously.

Y exclaims that X has succeeded, and Lysandre is flabbergasted that such a thing is even possible. He watches with amusement as the five Mega Pokémon begin attacking Zygarde, and thinks it is really a pity, since he for sure will be taking away the life force of the bearer of such tremendous power. With that, he orders a Dragon Pulse from Zygarde, which hits Salame square-chested. To his surprise, the attack barely scratches the Mega Charizard X, an it turns out that Y has commanded Veevee to shroud the area with Misty Terrain, which halves the damage of dragon-type attacks. Y hopes that X will grab this chance to go full throttle, and indeed, X shows no sign of hesitation as he commands an Outrage from Kanga and Li'l Kanga.

Back on Route 10, Delphox eventually realizes that an electric charge has filled the area, and quickly alerts the Admins that they are having intruders. At that moment, the fire fox catches sight of movement in the nearby rocks, and immediately throws out its branch to generate a blast of flames. However, this leads to an unexpected explosion, and both Chalmers and the female Admin become covered in flames. Desperately trying to put out the flame on their clothes, the two wonder what is going on, and Chalmers finally realizes that they have been hit by Vivillons' highly flammable Powder when he sees that their intruders include the Lumiose Gymleader Clemont, his sister Bonnie, the Santalune Gymleader Viola, her sister Alex, and the group of Sky Trainers led by Yvette whom they have once mind controlled…