Night time has fallen in Kalos. At Geosenge Town, X keeps himself hidden behind one of the cottages, and spies on the activity in town. Indeed, just as the image captured on Clemont's glasses suggests, Geosenge appears to be where the headquarters of Team Flare are, since TF Grunts are basically on guard everywhere. In particular, security is tightest near the small path that leads to the inner part of town, which naturally implies that it is where the Secret HQ is located. X wonders if he should simply charge right in or bypass the guards by sneaking in from the hillside, but before he could decide on his move, someone Pokés him from behind, causing him to bolt that he has been discovered. He quickly sends out Kanga to fight, but soon realizes that it is not a Team Flare Grunt but Emma.

Unfortunately, the little drama has already caught the attention of the Grunts nearby, and X has no choice but to send out his team to battle. Calling for a Mega Punch from Kanga, Shadow Punch from Lasma, and Wild Charge from Elec, X quickly stuns the Grunts and their Noibats. He then follows up with a Bite from Marisso and an Incinerate from Salame, and easily knocks out his opponents.

Emma applauds his skills, and X is curious to know why she has come. Emma simply grins that it is because of Mimi, and at that moment, the little Espurr pops its head out from Kanga's pouch, much to X's surprise. He wonders when it got there, and Emma reaches her arms out to Mimi. However, the Espurr seems reluctant to leave the pouch, and Emma can understand why since it must feel safer to be inside. She decides to let it be for now, and giggles that since Mimi wants to stay with Kangaskhan and she will always stay with Mimi, she might as well go along with X. Without another word, she starts walking towards the city center, and X yells out for her to stop as it is dangerous. However, his warming comes a little too late, and two other Team Flare Grunts have spotted them. The two each command a Goomy to attack with Muddy Water, but before the moves hit, Emma calmly lifts Mimi's folded right ear, which instantly sends off a powerful burst of psychic energy to blast off the Grunts and their Pokémon.

X and Kanga are both astonished by what Emma did, and Emma grins that she is no weak girl. Continuing on their way towards the inner part of town, Emma reveals to X that she used to live on the streets of Lumiose City by herself. Although she had parents and a family, she was horrified by their cruelty and thus ran away from home. On the streets, horrible things lurked everywhere as well, but at least she was protected by the Pokémon she befriended, which made living on the streets better than returning back home. Emma remarks that there were also other kids like her, and together with the Pokémon that protected them, they were known as the Lumiose Gang.

X wonders how Emma ended up at Cassius's place, and Emma replies that one of the kids in the gang knew Cassius. When the kid told her that at Cassius's place, no one judged and there were no horrible things, she decided to see for herself and it turned out to be true. X wants to know if Cassius is a good person, and Emma responds with a question, asking if a good person is equivalent to someone who doesn't horrify her. X supposes that it is, and Emma states that Cassius is a good person in that case. She grins that she likes Cassius a lot, which is why she really hopes to help him out. Unfortunately, she really has no talent in the Pokémon Storage System and couldn't really do much for him like the others, which was why she has been taking up part-time jobs. With that, she reaches into her pocket for something, and shows X what is apparently a recruitment leaflet. At that moment, Emma notices tears welling up in X's eyes, and wonders what is wrong. X quickly brushes it off as nothing, and Emma says they seem to have arrived at where X intends to go. Indeed, in front of them lies a metallic door embedded in a stone block, which most likely leads to Team Flare's headquarters. Emma picks Mimi up into her arms as X retrieves Kanga into its Pokéball, and the boy begins to figure out how he could get inside the door.

Inside the headquarters which is situated underground, Celosia spies on X and Emma via the security camera, and mechanically states that she must get rid of the intruders. Behind her, Mable wonders if she is alright, and Aliana giggles that Celosia has not rested at all after she moved in the 'Tree'. However, Celosia pays no heed to their words, and simply keeps her attention on the monitor screen. Annoyed that she is ignored, Mable scoffs that she was just trying to offer help in warding off the intruders, and Aliana giggles that they are really not trying to steal credit.

At that moment, something slashes towards Mable and Aliana, and the two Scientists bolt backwards in horror, narrowly missing what turns out to be the sharp blade on Bisharp's forearm. Bryony, who owns the Bisharp, steps into the scene, and Mable hollers that what she did was extremely dangerous. Bryony keeps a cold demeanor however, and tells Mable and Aliana to return to their assigned positions and stop barging into other people's business. Still shaken by the terror of nearly having their throats slit, Mable and Aliana decide not to argue and scurry out of the room with a cold sweat on their foreheads.

Bryony watches as Celosia repeatedly mutters to herself how she needs to rid of the intruders, and sighs that wielding Aegislashs's spectral powers for prolonged periods apparently affects the user as well. The fact that Celosia managed to stay sane for so long and complete her mission through it all makes her a really remarkable comrade. However, the mental stress she has accumulated in her current state makes the odds of winning extremely low, and the only way to raise it back up is to have a proper rest. With that, Bryony gets Bisharp to deliver a blow behind Celosia's neck to knock her out, and catches her companion as she falls unconscious.

The green-haired Scientist then steals a look at X on the monitor screen, and decides to let the boy in if it is what he asks for. She hopes that X would not regret his actions, and presses a button to lift the entrance's security lock. Immediately, the metallic door slides open, and X nearly tumbles into the opening. He tells Emma to stay cautious as they begin to make their way in, but he himself soon steps on a glowing panel, which Emma is too late to warn him about. In the next instant, X finds himself teleported to another room, and comes face to face with not only Xerosic but also Lysandre, who is fully geared up in a cybernetic suit. Slightly startled by the boy's unexpected arrival, Lysandre turns to face him and voice out his amusement that he has come alone. He remarks that X is no doubt a chosen one as well, and formerly introduces himself as the man who leads Team Flare.

In another room, Bryony sets Celosia to rest, and makes her way over to a transfer pod that leads directly above ground. She informs two Grunts that she shall be at the ruins to stay guard until the Ultimate Weapon surfaces, and proceeds to activate the propellers under her boots to begin escalation. She exits the ground via a secret opening between rock boulders, and continues her rise to midair where she gets a full view of Geosenge Town. In its center where the ruins are, three fang-shaped rocks stick out from the ground in a triangular pattern and point towards the sky. Bryony muses to herself that in between the three rocks is where the 'Sprout' will spurt in a few minutes. Having absorbed the life force it needs, the 'Sprout' will become a 'Bud', and as it bursts with energy, it is said to blossom into a 'Flower' with six petals, which shall unleash its life force and completely destroy every corner of Kalos. By then, the time filled with ugliness and chaos will come to an end, and a colorful future of beauty and harmony shall bloom.

Back at Laverre City, Gurkinn concludes his training session with Y, Tierno and Shauna, and compliments them for their hard work. He grins that their improvement is clear and evident, and the kids thank him for his guidance. Gurkinn recalls how the three aimed to be a Sky Trainer, Dancer and Furfrou Stylist, and muses to himself that their dedication to their individual dreams obviously manifested during their training as well, which made it so much more effective. In particular, Y's astute senses really impressed him, and he wonders if she would be a suitable candidate to pass the Keystone to. Stealing a look at his Mega Glove, the Mega Evolution Guru ponders on the thought, and is curious to know what Diantha and Korrina would think.

Just then, Trevor frantically enters the scene, and runs towards the group as he cries that everybody needs to calm down. Shauna frowns that Trevor should be the one to calm down, and Y wonders what is going on. Trevor hollers that X has vanished, and after a brief moment of silent bewilderment, Shauna, Tierno and Y all become frantic like Trevor. Y grabs Trevor by the collar and demands to know what he means, and Shauna voices out her disbelief as she thought X was still sulking inside the tree hole. Tierno tells Trevor to elaborate, and the orange-haired boy says he has found clues to X's whereabouts. He gestures to Klefki, who holds up a pair of glasses, and Shauna notices rock structures on its reflective surface. Trevor states that it is a scene capture of Geosenge Town, and explains that the glasses belong to Clemont, who has gone missing and is thought to be captured by Team Flare. He reminds everyone that Clemont's glasses can display images captured by the camera on his Aipom Arm, and both Shauna and Tierno immediately realize that X must have seen the scene capture and set off to Geosenge on his own. Hearing that, Y becomes both furious and worried, and cries that X is one big fool.

Back at the Team Flare Secret HQ, Lysandre sends out his Mienfoo and Pyroar, and X calls forward Marisso and Salame to fight. X recalls hearing about Lysandre from the others, and feels a surge of rage towards the man, who has now admitted to be the Boss of Team Flare. He demands to know why he destroyed Vaniville and took away everything from the everyone, and Lysandre, without a hint of regret, states that it is for the sake of a beautiful world. He gestures towards the column-like device behind him, which has multiple connecting tubes and is known as the Absorber, and reveals that it is currently draining the bioenergy of Xerneas to fuel the Ultimate Weapon. He knows that X must deem 'taking' as equivalent to something bad, but the fact is, he is 'taking' in order to allow harmony to be born, which one cannot deny is fundamentally beautiful. With that, he shows X the Keystone embedded in his ring, and X gasps in realization that it was the same one Team Flare snatched from Korrina. Lysandre grins that he was 'given' the Keystone to create a beautiful world, proceeds to activate it to Mega Evolve his Gyarados.

The Mega Evolved sea serpent towers over X, and the boy grabs his own Mega Ring. The image of Korrina lying on the hospital bed flashes across his mind, and he also recalls Gurkinn's words that one could only Mega Evolve one Pokémon at any single time. Stealing a glance at Kanga, Elec and Lasma, who are also looking up at him inside their Pokéballs, X wears a determined look, and makes up his mind about whom to use.

Meanwhile, Emma has reached a dark underground corridor, and wonders where it leads to. She asks Mimi what they should do, but the little Espurr simply glances back at her with its big eyes. Suddenly, she hears some heavy breathing, and quickly looks around for its source. Behind her, a huge man held captive inside a cell mutters with a low voice, and says it is necessary to take back the Key...