Seeing the Mega Stone at the tip of Salame's flaming tail, X's childhood companions gap their mouths wide open and exclaim in disbelief. Tierno, Shauna and Y usher forward for a closer look, and end up crushing Trevor beneath them. Y wants to know if Salame has had the stone all along since their first encounter, and X believes it to be the case, stating that Elec also went in search of the Manectite out of its own will.

Xerosic finds it absurd that the kids are dwelling on the topic, and reiterates with annoyance that their investigations have shown no evidence of Charizard being capable of Mega Evolution. However, Green voices out his disagreement, and Xerosic sees that the young man has also come around. He challenges Green to justify his claim, and Green proceeds to fish out a ring tied around his neck on a strap, which to the Vaniville kids' astonishment bears a Keystone. At the same time, Green's Charizard reveals that it is also holding a Mega Stone at the tip of its tail like Salame, and Trevor is bewildered that Green is one of the Successors of Mega Evolution. Upon a closer look, Tierno and Shauna notice that the Mega Stones of Green's Charizard and Salame are of different colors, the former a red and blue tone while the latter a black and blue hue, and X realizes that it is indeed the case.

Caught between surprise and humiliation, Xerosic wonders which is the real Charizardite, but on a deeper thought, decides that he may still be right and neither is a real Mega Stone for Charizard. He proceeds to send forth his quartet of Crobats to attack, and Malamar begins to lash out as well. Green's Charizard quickly takes on the Crobats, and X gets Salame to stop Malamar by clamping on its tentacles with its fangs. Y prepares to help, but Green suggests she leave the scene to him and X and head off to the Pokémon Village with the others first. As Xerosic has said, he is keeping them away from the Village in an attempt to redeem himself, which implies that something more sinister is going on at the Village. Y agrees, and takes out an Awakening to heal Croaky from its sleep status. Croaky then blinds the enemy with a Smokescreen, and Y takes the chance to slip off with Tierno, Trevor and Shauna. Xerosic grunts in frustration as he chokes on the smoke, but to his dismay, the situation gets even more difficult for him, as Salame begins to glow and in a flash of light, evolves into a Charizard.

The red-haired Scientist is furious that everything is working against him, and just then receives an intercom message from Aliana. Xerosic barks that he has no time to chit-chat, and Aliana giggles that they are well aware of it. She also states that they know four of the kids have slipped away with Smokescreen and are on the way to the Pokémon Village. It turns out that Aliana along with Mable, Bryony and Celosia are hovering just above the scene, and staying airborne with the propellers under their boots. Xerosic is startled by their arrival since they should be transporting the bioenergy sources, but Aliana giggles that they have completed the task long ago and are there because they believe that Xerosic needs help. With that, the four female Scientists swoop down towards the Vaniville kids who are heading to the Pokémon Village, and pick them off one by one to split them up. Y, being the only one left on her tracks, is alarmed by the sudden scream of her friends and turns around in shock to find herself alone. Before she could comprehend what is going on, Aliana's Diggersby materializes and lashes out at her with its fist-like ears.

Back on X and Green's side, while Green's Charizard is keeping the Crobats at bay with its Flamethrower, Salame gets restrained by Malamar's tentacles and grits its teeth in frustration. Green notices the hesitation on X's face, and wants to know what is on his mind, since Salame is clearly waiting for his cue to Mega Evolve. X places a hand on his Mega Ring, and frankly couldn't think of a good reason why he subconsciously doubts the authenticity of Salame's Mega Stone after all this time. The fact that Salame scouted it out on its own and protected it so closely since the beginning is more than enough proof that it is a genuine Charizardite. Now that Salame has emerged from its Pokeball after coming to terms with its destiny, it would be ridiculous for him as its trainer not to respond to its calling. Moreover, it is time that they bring down Xerosic, bring down Team Flare, and take back a peaceful tomorrow for the sake of humans and Pokémon. With that, X puts on a determined look, and Green grins in response as he slips on his own Mega Ring. Calling for the light of their Keystones to intertwine with that of the Charizardites, Green and X raise their arms, and Mega Evolve their Charizards, with Green's gaining longer horns on its head and wings on its arms while X's turning pitch black with blue flames spewing out from the corners of its mouth.

Meanwhile, Aliana's Diggersby rams down with its fist-like ears again, and Y narrowly jumps out of the way. Aliana giggles that it is a pity that the attack missed, and Y glares at her with rage. The girl calls out to her friends and wants to know if they are alright, and Shauna, having heard Y's cry, hollers that they are far from alright. However, she refuses to give up, since she is facing the foe who has manipulated her to turn against her own friends before. With a determined look, Shauna stands firm, and commands her Skitty to take on Celosia's Doublade. For Tierno, his dancing moves are helping him evade the fire attacks of Houndoom, and Mable is clearly getting annoyed by that. The burly guy states that he will not yield to their evil schemes, and gets Corphish to smack hard on Houndoom with its pincers, causing the black hound to wince in pain.

Things are not so smooth on Trevor's side unfortunately, and the boy finds himself cornered by Bryony's Bisharp. He fights to control his tremble, and wills himself to work hard like his friends are doing. As Bryony towers over him, she remarks that neither they nor the Watcher could interfere with them this time, and Trevor gets confused by her words. By the Watcher, the Scientist is clearly referring to Zygarde, who has supposedly fallen into the hands of Team Flare after it was captured by Essentia, but her tone suggests that it may not be the case. Her use of the phrase 'this time' also implies that they are repeating a deed they have done in the past, which Trevor eventually realizes has something to do with the Ultimate Weapon. At that moment, Bisharp strikes forward with its blade-like arms, and Flabebe expels a shower of petals to fend off its attacker. Trevor grabs the chance to slink off, and knows that he must inform his friends of what he has learnt as soon as possible.

With their combined fire attacks, Green's Mega Charizard Y and X's Mega Charizard X have successfully knocked out Xerosic's Malamar and his quartet of Crobats. Although the red-haired Scientist is stunned by his defeat, he is more devastated by the fact that Charizard really has the ability to Mega Evolve. To make things worse, it has two different forms, both of which are completely unbeknownst to Team Flare, which shows how inadequate their science and organizational skills are. He bangs his fists on the ground in anguish and disbelief as the hard truth sinks in, and Green comments that one who thinks too highly of himself will eventually self-destruct. Knowing that Xerosic no longer has the Pokémon or will to fight, X decides to go after Y and the others, and the two swiftly go airborne on their Mega Charizards.

Soon enough, they spot Y and Croaky, who are battling with Aliana's Diggersby. At that moment, Green spots Trevor being edged towards a cliff by Bisharp and alerts X to it. X realizes that the Scientists must have intercepted his companions on their way to the Pokémon Village. The two decide to split up, and while Green goes to help Y, X swoops down with Salame just as Bisharp lunges forward to strike. The black Mega Charizard instantly fries Bisharp with a blast of flames, and picks Trevor up into its arms as it hovers back up again. Trevor is overjoyed that Salame has evolved and Mega Evolved as well, and X wants to know where Tierno and Shauna are. Trevor replies that he has no idea since they were forcefully split up, but believes that they are fighting Mable and Celosia. He then informs X anxiously that Team Flare is apparently planning to activate the Ultimate Weapon again, and Zygarde may not have fallen into their grasp after all.

Before X could react to the news, a powerful beam strikes down from above and hits the area right next to them. The explosive blow throws Green and his Mega Charizard Y backwards, and both X and Trevor exclaim in bewilderment as they see Yveltal dive down from the skies. The bird of death fires another powerful beam straight towards Green, but the attack is neutralized as Y cuts in with Xerneas just in time. Y wants to know if Green is alright, and the young man finds it ironic that she ends up being the one helping him when he was supposed to help her. Speaking through telepathy, Xerneas tells Y to leave the scene as it shall now engage in a fight with Yveltal without human interference. Y voices out her support to Xerxer, and wishes it good luck as she hovers off on Fletchy. She joins the others on the ground, and is astonished to learn from Trevor that Team Flare is scheming to activate the Ultimate Weapon again.

Trevor frankly doesn't understand how Team Flare plans to fuel the Weapon since the Absorber has been destroyed by Xerxer and both legendary Pokémon are currently fighting, which makes it impossible to harness any bioenergy from them. However, Y suddenly remembers what happened to the wild Scyther which was the battle companion of X's Pinsir, Rute, as well as the many wild Pokémon Shauna and Tierno saw on Route 19. According to what Green said, they were all drained of their bioenergy, which was clearly Team Flare's doing. Trevor thinks it makes sense, and believes that Team Flare must be looking to gather a large sum of Pokémon. At that moment, X recalls Xerosic saying that the Pokémon Village is home to many Pokémon who once suffered from human cruelty, and everyone instantly realizes that Team Flare is planning to use the wild Pokémon at the Pokémon village as fuel to the Ultimate Weapon.

Meanwhile, on Route 10, also known as the Menhir Trail, Pokémon from the Pokémon Village are being tied against the stone blocks by Team Flare Grunts. One of the Pokémon, which is actually Shauna's lost Furfrou, sits helpless as it gets a feeling that something bad to going to happen. Suddenly, it spots a Delphox walking among the Team Flare Grunts, and instantly recognizes it as the same Fennekin which Trevor lost during the Vaniville incident. Furfrou makes an attempt to call out to the now fully evolved Pokémon, but the fire fox simply walks on and pays no heed.

Somewhere in the Pokeball Factory, Essentia curls up on the ground and holds her head in agony as her consciousness slips back and forth between her artificial intelligence identity and that of her true self…