Out in the countryside of Route 18, the legendary Xerneas and Yveltal shall once again clash. Standing next to their Charizards, who have reverted back from their Mega states, Green, X, Y, and Trevor watch as the Pokémon of life who 'gives' and the Pokémon of death who 'takes' stare down at one another. Yveltal lets out a shriek, and fires a bright red beam which explodes as it connects with Xerneas. The move instantly turns the surrounding terrain barren, and Y exclaims that it is just like what happened at Vaniville. She wagers that it must be the signature attack of Yveltal named 'Oblivion Wing', and Trevor is shocked that she knows about it. X believes that she must have learnt of it from Alexa's files again, and Y admits with a nod. She explains that the move not only deals great damage but also steals the health points of its target when it hits.

As the group watches, Yveltal makes its next assault and suddenly vanishes into thin air, much to everyone's astonishment. It then reappears behind Xerneas, and rams its tail hard into the big blue deer, nearly throwing it off its feet. Green recognizes the move as Phantom Force, and Trevor starts to get worried since Xerxer is getting beaten up by Yveltal quite aggressively. He asks Y if Xerxer's bioenergy has fully recovered yet, but Y, who is frustrated by the same thing, states that she has no idea. At that moment, she hears Xerneas's voice through telepathy, and the legendary deer wants to know why she is still around. It assures her not to worry and tells her to set out to the Pokémon Village as soon as possible. As it speaks, it rears its head with a glow, and the power it emanates instantly causes plantation to sprout and bloom around it. X, Y, Trevor and Green watch with bewilderment, and Xerneas explains that it 'gives' wherever Yveltal 'takes', and Yveltal 'takes' wherever it 'gives', which is their way of existence.

Green realizes that this must be how the two creatures maintain their power balance and it explains why a clash between them could last a thousand days. X rationalizes that since Xerxer is lending them its powers, the balance has tipped towards their side. However, Xerneas states that things are not as simple, and reminds them that the enemy is most probably working on the Ultimate Weapon again, which clearly calls for more urgent attention compared with its current fight against Yveltal. Y decides that Xerneas is right, and suggests X and Green leave for the Village immediately while she and Trevor go and help Tierno and Shauna. X agrees with her plan, but Trevor suddenly realizes that Diantha is missing. Green tells him not to worry, and reveals that the young woman has secretly headed off to the Village first after she woke while they were keeping Xerosic busy. X climbs onto Salame, and tells Y and Trevor to join them as soon as they have gathered Tierno and Shauna. Y reminds them to stay alert, and the two boys swiftly go airborne on their Charizards.

Nearby, Diantha watches as the pair of Charizards fly across the sky, and feels glad that Green and X are advancing towards the Pokémon Village. She thinks it is a pity that Malva's attempt to thwart her and ambush the kids with Yveltal amount to nothing after all, and wears a smirk as she glances towards the fire type Elite 4. However, Malva seems happy enough that she currently has the Kalos Champion immobilized by Talonflame's burning wing at her throat, and believes that the kids will have their share of fun when they arrive at the Pokémon Village. Her remark confuses Diantha but the pink-haired woman decides to change the subject and reveals that her Talonflame was not merely meant to thwart her. Boasting wings that are blade-sharp and flame-coated, it was also meant to take her down. With that, Talonflame delivers a brutal slash at Diantha's face as Malva bids her farewell.

Meanwhile, Green and X have soared past Snowbelle City and are about to reach the Pokémon Village. However, something is bothering X. According to what Xerneas said in Anistar, the Pokémon called Zygarde would show up for suppression whenever it senses the other two legendaries using their powers. From what Trevor learnt, it apparently did not fall into the hands of Team Flare as well. That said, he wonders why it did not appear when Xerneas and Yveltal clashed and fought. Flying past a heavily forested area, the two finally arrive at their destination. Yet, contrary to what Xerosic said about it being a paradise for Pokémon who have suffered ill treatment from humans, not a single Pokémon is in sight.

X soon spots what appears to be a work station, and sees a group of Team Flare Grunts heavily beaten up. He wonders if it is the work of Diantha, but Green isn't so sure. The young man carefully scans their surroundings, and suddenly senses something rapidly approaching from behind. He quickly alerts X to it, and the two send out Rhyperior and Marisso for defense. However, as the creature ambushing them comes into view, Green bolts with recognition and astonishment. Before he has a chance to react, the white humanoid creature which has a purple tail charges forward as it swings around the two spoon-shaped weapons it wields, knocking back both Rhyperior and Marisso. X gets ready to command an attack from his recently evolved Chesnaught, but Green stops him and expresses his surprise that the being has ended up in Kalos. X realizes that Green knows their attacker, and Green reveals its identity as Mewtwo, the genetic Pokémon whom he has battled alongside with at the Kanto region's Sevii Islands.

X wants to know if it is their comrade in that case, and Green fervently calls out to Mewtwo, identifying himself as a Kanto Pokedex Holder. However, Mewtwo seems oblivious to his words, and starts to conjure up a psychic tornado after connecting its two spoons together. The powerful swirl spins Green, X and their Pokémon around in midair and hurls them down onto the ground as it stops. At that moment, Lysandre appears on his Gyarados, and thinks it is splendid that someone is helping him get rid of the intruders. X grits his teeth in anger as he sees the Team Flare Boss, and Green demands to know if he is the one manipulating Mewtwo. Lysandre muses at the name, obviously not knowing about it beforehand, and addresses it as the legendary Pokémon who protects the Village. X wonders what he means, and it turns out that the behavior of the Village's Pokémon have baffled Lysandre when Team Flare first set foot in the area. According to what is said about the Village, the inhabiting Pokémon have all been victims of human cruelty and should naturally be fearful of humans. However, despite Team Flare's arrival, not a single Pokémon went into hiding, and Lysandre realized that they must be protected by a certain being, who has kept itself hidden all this time and only showed itself the night before.

Green believes that it was probably the time Team Flare kidnapped the Village's Pokémon and brought them to the Ultimate Weapon, and says such an act would clearly anger Mewtwo and make it blinded by rage. Lysandre is astounded that Green knows about their plan about the Ultimate Weapon and becomes furious. On a deeper thought, he decides that it doesn't really matter because there is nothing they can do about it. He points out that Mewtwo is apparently conserving its powers as it fought his Gyarados, Pyroar and Mienfoo, and his team would probably have a hard time winning. However, with Green and X as additional opponents, no matter how skilled Mewtwo is, it would eventually tire itself and after it knocks the boys out, he shall make it his own fighting force.

At that moment, Mewtwo throws a barrage of energy globes into the sky which soon come raining down towards Green and X as psychic beams. Green recognizes the move as Psystrike, and X hurriedly commands a Spiky Shield from Marisso while Lysandre watches with a smirk. Yet, right before the beams connect, Mewtwo changes their course and directs them onto Lysandre and his Gyarados instead, hitting them hard. The Team Flare Boss winces in pain and disbelief as blood dribbles out from the corner of his mouth, and in that instant, Mewtwo begins to glow with a seven-coloured light. X and Green bolt in recognition at the familiar glow, and as it washes over Mewtwo, the genetic Pokémon Mega Evolves, losing its tail to become more streamlined while gaining a long appendage which extends out from the back of its head. Green realizes that the Mega Evolution means someone must be resonating with it, and soon spots a silhouette on top of a nearby cliff. Lysandre, who is trembling with both pain and frustration, shares the same realization and decides to activate something with a secret device he is holding. Meanwhile, at Cassius's cottage at Camphrier Town, one of the punk girls informs him that Emma's PC storage is being accessed. Cassius wants to know if the location can be identified, and another girl replies that it is in the proximity of Route 22. She adds that the Pokémon being deposited a few days ago is now being withdrawn, and Cassius really wishes to know what Emma is up to. He decides to head to Route 22 directly to find out, and begins to set off with his team of punks in his van.

Back at the Pokémon Village, Lysandre's Mienfoo and Pyroar are having a hard time landing their attacks on Mewtwo, and both Green and X are bewildered by the Pokémon's markedly heightened speed after Mega Evolution. Suddenly, the entire ground begins to rumble, and in the next instant, the earth cracks and Zygarde breaks out from beneath…