At the Pokémon Village, the earth shatters into pieces as Zygarde breaks out from underneath with Essentia riding on its back. Green gasps at the unexpected reemergence of the legendary Watcher, and X can see that Essentia has indeed caught it successfully at Anistar, which makes him wonder why Bryony didn't seem to be aware of it according to Trevor. Lysandre, who continues to fight Mega Mewtwo with his Pyroar, Mienfoo and Mega Gyarados, reveals that Essentia has deposited Zygarde into the Pokémon Storage System after its capture. As a result, they became unable to track down her whereabouts.

X is astonished that Essentia doesn't work under Team Flare's commands, and Lysandre explains that it was thanks to the idiotic humanitarian beliefs of their Scientist, Xerosic. It turns out that when equipped with the Expansion Suit, the test subject inside is hypnotized and an artificial intelligence that works under Xerosic's command takes over the body. In order not to cause any permanent strain on the test subject's body and mind, the suit is designed to have a limit to its activity scope and time. However, repeated activity will weaken the suit's hypnotic effect and there is a chance that the test subject will regain self-consciousness and break free from control. To rectify this flaw, Lysandre has lifted the limit placed on the suit, and with the special control device he currently has at hand, he now has full control over Essentia, which enabled him to have her retrieve Zygarde from the Storage System. To put it simple, the test subject inside Essentia is now nothing more than a mindless pawn that obeys his every command.

Lysandre thinks X would agree that science is such an amazing thing, and X grits his teeth in anger at the man's mockery. Just then, a voice comes on to comment that godless science leads to the birth of a devil with wisdom, and says it seems the Scientist named Xerosic hasn't gone too far and still has a chance to return from his erroneous path. An old man with moustache and sunglasses then shows up, and Green, who is familiar with the man, is pleasantly surprised that the Kanto Gymleader of Cinnabar has also come to Kalos. The old man, Blaine, explains that he has reunited with his brother Mewtwo after so many years, and has recently decided to settle down at the Pokémon Village with it. However, it seems that during his short absence, something has managed to infuriate his brother and made it fuming with rage.

Blaine points out that he himself was a devil with wisdom once and has devoted himself to science. However, he now realizes that it is easy to overlook mistakes based on science alone, and asks to join forces with Green, which the latter gladly accepts. Lysandre shakes his head in disagreement upon hearing Blaine's words, but decides that it is no use arguing. He commands a Land's Wrath through his control device, and Essentia immediately relays the message to Zygarde. The white hexagons on Zygarde's body begin to glow intensely, and in the next instant, the entire ground beneath them explodes into a million pieces, hurling sharp boulders at Green, Blaine, X and their Pokémon.

Meanwhile, on Route 22, which is also known as Detourner Way, Cassius's punks alert him that an explosion has just gone off in the direction of Route 20. Cassius knows that something big must be going on, and quickly steers his van to the direction, despite protest from his punks that they should be looking for Emma instead.

Back in the woods where Malva has ambushed Diantha, Talonflame's deadly slash has been blocked off by Gardevoir, who has unexpectedly popped out from its Pokeball. Malva then realizes that Diantha has activated the Pokeball with the bottom of her heel, and Diantha explains with a grin that an old friend once taught her this trick, which was used by a certain trainer long ago in a faraway region when he was trying to break free from a critical moment. The Kalos Champion begins to reach for her Mega Charm, but discovers with astonishment that it is missing. Malva reveals with a smirk that it is currently in her hands, and feels glad that she may use Mega Evolution with it just like Lysandre. With that, the fire expert goes airborne on Talonflame, and Diantha quickly gives chase by levitating on Gardevoir's psychic powers.

Nearby, Y and Trevor ride on Solsol and continue to search for Tierno and Shauna. Suddenly, the ground below them softens considerably, and both Solsol and Veevee get their feet caught in the mud. Aliana shows up and laughs that it really spares them the time to hunt when preys make a comeback themselves, and Y realizes that they have been ambushed Diggersby's Rototiller. Seeing that another Scientist, Bryony, is also present with her powerful Bisharp, she quickly gets Veevee to attack with Disarming Voice. However, despite scoring a direct hit on Aliana's Pumpkaboo, it remains unfazed and retaliates with Seed Bomb, which causes an explosion on the softened soil and throws the Sylveon off its feet.

Aliana giggles that tilling the soil in advance really gives them an advantage, but her laughter is cut short when Trevor commands a Razor Leaf from Flabebe, which manages to knock out Diggersby in one hit. Both Aliana and Y are astonished by the power of the attack, and Trevor explains sheepishly that Rototiller powers up grass-type moves regardless of ally or foe. At that moment, Flabebe begins to glow and evolves into a Floette in a flash of light, much to Trevor's bewilderment. He doesn't understand how it would evolve when it barely fought and merely guarded him, but Y slaps him on the back, and reminds him that Flabebe not only played a part in fighting the Tyrunt for the Manectite but also blasted Lysandre off when they were trying to pull out the Ultimate Weapon's key and subsequently received special training under Master Gurkinn. She points out that Trevor and Flabebe have been fighting all this time and they are actually much stronger than they think.

Y's compliment causes Trevor to blush, and he thanks her for her encouragement. Wearing a confident look, he believes that he is capable of handling the Scientists himself, and wants Y to go help X since her powers are definitely needed in his battle against Lysandre. Y agrees to his proposal, but reminds him to take shelter in case it gets too dangerous. She then flies off on Fletchy, and Trevor urges her to stay safe as he will do himself.

Back at the Pokémon Village, Zygarde's powerful attack has created a giant crater on the ground, and both Green and Blaine are severely injured from their attempt to protect X. Blaine lays sprawled across the fallen boulders, and Lysandre notices that Mewtwo has become motionless despite keeping its Mega state. Working on a hunch, he commands Gyarados to fire a blast at Blaine, and as the Cinnabar Gymleader gets hit, Mewtwo instantaneously takes the same amount of damage, forcing it to revert to its usual form. Lysandre is amused that the old man and Mewtwo are so in sync with one another, and proceeds to have Essentia order a Camouflage from Zygarde. In a blink of the eye, the giant green serpent vanishes, and X exclaims that it has not only changed its type but also literally camouflaged itself by turning its colour to match its surroundings.

Mewtwo stays on guard as it looks around, and Blaine weakly calls out to it. After exchanging a nod, Blaine tosses Mewtwo another Mega Stone in exchange of its current one, and calls for the light of the Mewtwonite X to intertwine with that of his Keystone. At that moment, Lysandre orders a Crunch from Zygarde, and the giant serpent materializes right next to Mewtwo to clamp its jaws down. In that split second, Mewtwo Mega Evolves again but takes on a different and bulkier appearance, wielding a psychic spoon which it uses to fend off Zygarde's attack. X and Green gasp that Mewtwo also has two forms of Mega Evolution like Charizard, and are shocked that it can embody both at the same time. Blaine explains that while Mega Evolution only occurs once with one Keystone in a single battle, the part of him that remains in Mewtwo and that of Mewtwo in him make this special situation possible.

Standing on his Mega Gyarados, Lysandre sees that Mewtwo has become physically oriented with this Mega form. However, it is apparently struggling to hold back Zygarde's assaults, which shows that there is a great discrepancy in power between the psychic mutant and the Kalos Watcher. X looks over to Essentia, and sees that she is beginning to slump forward. He rationalizes that Lysandre's control must be taking a toll on her body, and he may just be able to severe the man's indirect control on Zygarde if he strikes her down.

He orders a Pin Missile from Marisso, and the Chesnaught quickly fires a barrage of missiles onto Essentia, shattering her helmet and sending her tumbling down. Unfortunately, this doesn't stop Zygarde from attacking, and X thinks he will need a close-up attack to disable the Expansion Suit's function. However, before he could make another move, Lysandre intercepts with his Mega Gyarados and strikes him down along with Marisso. At that moment, something slashes at Gyarados's face, and X sees that Y has come to assist him with Solsol. With Gyarados distracted by the Absol, X hurries over to Essentia. Yet to his horror, he sees that the person inside the Expansion Suit is no other than Emma, the girl whom he met through Cassius.

Still in the air on Fletchy, Y notices an aerial clash nearby and soon sees that Diantha is chasing after Malva. She decides to help, and gets Fletchy to unleash a blast of flames, which sears at Malva's hand and forces her to drop the Mega Charm she holds. The item falls to the ground below where Green is, and the young man quickly recognizes it as Diantha's personal Mega accessory. Holding the Mega Charm next to his own Mega Ring, he contemplates on the saying that Mega Evolution only be activates once per Keystone per battle, and wonders if this concept can be their key to victory.

For X, he still has a hard time believing that Emma is the test subject inside Essentia all this time. Fervently calling out to the girl, he urges her to get out of the Expansion Suit and attempts to help her disable the switch. However, to his shock, Emma stops him and says she will not come out of the suit. X cries that she doesn't understand the situation, and tries to explain that she has been under hypnosis and was exploited by Team Flare. Yet, Emma reveals that she has full recollection of everything she did while in the suit, and her words cause X to widen his eyes in disbelief.

Emma states that she has constantly been in fear, both at home and on the streets. Everyone keeps doing horrible things to her, and even when she calls out for help, no one ever comes to her aide. With the Expansion Suit on, she doesn't have to be afraid anymore because she can achieve anything, which is why she will not leave it. X argues that Team Flare is an evil organization that needs to be taken down, but Emma wants to know if she doesn't have to fear anymore if Team Flare is taken down. She questions if people will start being nice to her if Team Flare is taken down, and to that, X finds himself at a loss of words.

Back in the air, Y hovers over to Diantha, and the young lady thanks her for her help. However, she asks Y not to assist any further, as she shall take matters into her own hand and fight this battle against Malva as the Champion of Kalos…