At the Laverre Hospital, Cassius's team of punks helps him keep track of their progress by reporting the number of people rescued. With 14 people from Route 7, and 1 from the emergency center on Spikes Passage, they have 15 Sky Trainers. 29 residents have been found on Route 8, 30 if counting Y's mother, and that adds up to a total of 45 people, which is the exact amount of Vaniville locals who went missing after the town's incident. Cassius sees that all of the rescued residents have yet to regain consciousness, but Trevor thinks it is already fantastic that they have managed to rescue them all and even brought them to the hospital. He praises Cassius for being a benevolent man, and the punks immediately break out in laughter upon hearing the comment. Cassius sweatdrops and tells Trevor that he is clearly nothing of that sort, and says the credit really goes to someone else.

A girl's voice comes on to say that Cassius makes it sound like a big favour, but believes that when it comes to helping people in need, Gymleaders, or rather everyone, share the same responsibility. Trevor turns around in surprise to find three people approaching, and sees that the one who spoke is Valerie, the Laverre Gymleader, a girl in Furisode attire who is accompanied by her Mr. Mime. Next to her are Grant, the Cyllage Gymleader whom they have met, and his Aurorus; and Olympia, a woman in a starry gown who is also the Anistar Gymleader, and her female Meowstic. The three Gymleaders formally introduce themselves, and Grant remarks that they have just heard all about the red-suited people, or rather, Team Flare. Valerie sincerely sympathizes with what Trevor and his friends have gone through so far, and Olympia sighs that although it sounds embarrassing, they have really not been aware of Team Flare's activity until now.

Valerie states that she has actually seen the strange red-suited people lurking around the Poké Ball Factory in her city, and thinks it must be investigated upon. The truth is, she had no idea that both Viola and Korrina have fought these people until she contacted the other Gymleaders just now, and she is appalled to know that even Alexa has been ambushed. She is upset that no one told her of such things all along, and starts shaking Trevor repeatedly, asking if he understands how it feels to be kept in the dark. She reveals that she has actually tried to contact Korrina after the Tower of Mastery collapsed but has not been able to do so, which left her extremely worried. Now, watching how Korrina suffers, she really feels her heart break.

Trevor believes that Viola and Korrina have kept their mouths shut because they didn't know who to trust, and Cassius agrees with the thought. He points out that Team Flare has already infiltrated the entire Kalos and their people are apparently everywhere. He steals a glance at the doctors and nurses, and says he frankly doesn't know if they can let their guards down and trust everyone in the hospital either.

At that moment, Grant's phone rings, and he picks up to find Ramos and Wulfric calling. He learns that the two men will be arriving in 15 minutes, and tells Valerie and Olympia that they should go meet them outside. Valerie wonders if Clemont still could not be reached, and Grant admits it with a worried look on his face. To be honest, he starts to fear that Team Flare might have gotten to the Lumiose Gymleader as well. Shaking the thought off his head, Grant thinks the remaining Gymleaders should congregate and decide on how to deal with Team Flare as soon as possible, and heads out of the hospital to climb onto his Aurorus with Olympia and Valerie. He tells Cassius to take charge of the situation at the hospital, and Cassius assures him not to worry. Trevor notices that the two men are no longer at odds, and is surprised that they have become friends, but Cassius reveals that they are on good terms simply because he has agreed to pay the repair cost of the rock-climbing and cycling courses, which causes Trevor to sweatdrop.

Suddenly, they see Valerie running back to them in high spirits, and the Furisode girl zealously asks if Trevor has really seen the 'Tree' which was supposed to be the dormant forme of a legendary Xerneas. Trevor admits that he has, and Valerie says her city also has a symbolic giant tree which is 1500 years old. She gestures towards the large tree sitting right next to the hospital, and wants to know which tree Trevor thinks is greater. She slaps the boy repeatedly on the back as she asks him to compare their magnificence, coolness and grandness, and the boy gets slightly overwhelmed by her behavior. Before Valerie could continue, she is lifted into the air by Olympia's Meowstic, and the Anistar Gymleader nags that they should really get going. Valerie's Mr. Mime uses its psychic powers to help to bring its trainer back onto Aurorus, and Valerie directs her questions to Olympia instead, hoping that she will agree that the Laverre old tree is much greater.

Trevor sweatdrops as Valerie continues to pester Olympia, and watches as the three Gymleaders finally venture off. Cassius then wonders where the other Vaniville kids are, and Trevor points towards the nearby grassland, where Y, Tierno and Shauna are undergoing special training under the guidance of Master Gurkinn. Cassius sees that Chespin and Charmander are also practicing, but the Mega Evolution boy is nowhere to be found. Trevor sulks as he gestures towards the giant tree, and Cassius assumes that X has retreated into the tent again since Rhyhorn is resting next to the tree. However, Trevor actually meant the giant tree itself, and reveals that X has locked himself up inside the tree hole, even sealing the area off with web of plastic tapes.

Cassius bolts at the scene, and wants to know exactly what is going on. He is certain that Valerie would go berserk if she sees what X has done to the tree, and tries to tear off the tapes and approach the boy. However, Trevor quickly stops him, and tells the man to leave it to him instead. Raising his voice, Trevor calls out to X, and urges him to come back out. Yet, X turns his back away from the opening, and refuses to speak until he can be sure that he is talking to the real Trevor. Clearly, Essentia's shape-shifting earlier has left him paranoid, and he asks Trevor to tell him something only the two of them know to prove his identity.

Trevor struggles to come up with something, and suddenly spots Klefki hovering around X, the same one which was with Y's mother. He immediately remembers the Klefki he met at his uncle's home years ago, and recalls how the mischievous Pokémon collected not only keys but also screws and other domestic tools, dragging them across the floor despite their heaviness. X faintly recalls having heard of the story from Trevor before, and deems it good enough to prove the boy's identity. He wants to know what Trevor wants, and Trevor says he simply wishes to inform him of their situation. He mentions that the 15 Sky Trainers who attacked the helicopter have all been admitted to the hospital, and the Gymleaders have also gathered to work on a strategy to deal with Team Flare. Unfortunately, none of the rescued people have regained consciousness, which is why they still don't know where the enemy's headquarters are. They have thought about following the tracks of the truck which transported the 'Tree', but due to the heavy rain, the tire trucks are barely traceable and give them no clue as to where the truck went. Nevertheless, they have successfully freed the Vaniville residents from the enemy's mind control, and it has been a meaningful battle overall.

X pauses for a moment, and wants to know if it is really the case. He points out that not only Diantha has gone missing, but Korrina also had her Keystone snatched and the three Team Flare people managed to get away with the 'Tree', all of which are important losses. He sulks that the only reason the Vaniville residents got rescued was because Korrina risked her life to save them, while he basically just stood there and did nothing. He blames himself for being a total failure, and thinks his ability to wield Mega Evolution only adds to the shame.

Trevor is left speechless at X's rant, and gets emotional himself as he wonders what to say. Cassius decides to give X some time on his own, and pulls Trevor away from the scene. He wants to know when exactly X entered his current state, and Trevor replies that it was during the time the doctors ran their tests on Korrina at the hospital. Back then, they mentioned that despite the head trauma, Korrina's physical injuries were minimal. However, she has suffered a considerable amount of mental trauma, and upon hearing that, X suddenly began to throw up. Trevor recalls that X once told him when he first put the Mega Ring around his wrist, it felt as if he gained an additional brain and heart on his left hand, which illustrates just how powerful the mental connection must be between a trainer and the Keystone. Cassius figures that X must have envisioned himself in the same situation as Korrina, which caused his body to react, but thinks it is not the only reason that sent him back into dejection. All these years, X locked himself up because he believed that misfortunate would befall any Pokémon who came in contact with him. Now, he must think that not only Pokémon but also people would share the same fate.

Cassius gestures towards X's Mega Bracelet, and Trevor is shocked to see that X has once again placed a plastic tape over it. He feels sad that things have reverted back to the way they were after all they have done, and at that moment, he sees Marisso and Salame approaching them with Emma and her little Espurr. Cassius is glad to see that Emma is back, and suggests she informs them of her whereabouts next time so as not to worry them. Emma smiles as she points towards Marisso and Salame, who suddenly begin to flash and glow. In the next instant, they evolve into a Quilladin and Charmeleon simultaneously, and Cassius grins that it must be the result of their special training. Trevor breaks into a big smile and tells X to take a look at Marisso and Salame. However, X has his back turned against them, and Cassius comforts Trevor that the boy will eventually come out when he decides to.

Meanwhile, at the Team Flare Secret HQ, transportation of the 'Tree' is complete, and it sits silently on top of the giant Absorber, which has tentacle-like tubes that are designed to drain its energy. Standing next to his Gyarados, Lysandre gazes upon the dormant forme of the legendary Pokémon Xerneas, and is pleased that everything is finally ready. Xerosic confirms that all key aspects are set, and presents to him the Keystone they have obtained, which was thanks to Celosia's hard work. Upon Malva's request, he has fashioned the Keystone into a finger-ring, and Lysandre wastes no time to strap it on. Xerosic grins that it is a snug-fit, and believes that Malva would have really wanted to set it herself. The Scientist then helps Lysandre get into a cybernetic suit which has an arm-gear, three turbine-shaped devices that stick out from a back-armor, and a pair of special red goggles. Activating his suit, Lysandre gets himself psyched up, and states that the time has come to return Kalos to its beauty.

Xerosic feels moved by the scene and wipes off a tear of joy. He then steals a glance at Clemont, who has passed out, and orders two Grunts to dispose of him into the trash incinerator since he is of no use anymore. The Grunts proceed to dump the boy along with his bagpack into a garbage chute, and if the Lumiose Gymleader doesn't come around and find a way out, he will surely be burned into ashes along with the trash soon.

Back in the giant tree hole in Laverre City, X slumps against the floor and keeps replaying scenes of the recent incident in his head. When Y first heard of their plan, she strongly objected to it, since she deemed it more important to rescue the people under control first. She also questioned their chance of succeeding with a surprise attack, but he was so confident in himself that he didn't heed her concern. Thinking back on it, he has clearly overestimated his strength, which resulted in what happened to Korrina. The image of the Shalour Gymleader lying in the hospital bed flashes across his mind, and he lets out a cry of agony and frustration. With tears welling up in his eyes, he believes that if he has listened to Y's advice and prioritized the rescue of the Vaniville residents, Korrina's Keystone would not have been taken. In other words, he was the one who took away Korrina's Keystone.

At that moment, a voice comes on to state that he should find a way to 'give' in that case. X gasps with surprise that the tree is speaking to him, but soon realizes that it is something else. The voice states that 2000 years ago, power was given to this land in the form of a 'seed'. 500 years later, the 'seed' began to sprout and spent the next 1500 years growing. The voice reminds X that growth takes time, which length may be mind boggling occasionally. As a human, X also grows, but growth cannot happen if he keeps closing off his heart due to hurt. The voice urges X to open his eyes and look forward once more, and as someone who possesses, give to those who have lost.

The voice soon fades into distance, and the visage of Xerneas momentarily flashes in front of X's eyes. The boy finds himself feeling better all of a sudden, and soon senses the touch of something on his back. He turns around to see Klefki trying to comfort him, and thanks the little Pokémon, assuring it that he is alright now. He then notices a pair of glasses it is trying to show him, which seems to have something on its reflective surface. He checks on them to see the image of some regularly aligned rock structures, and finds them strangely familiar. Suddenly, he recognizes the glasses as those of Clemont, and recalls that they display images captured by the camera on the Aipom Arm. At that moment, he realizes that he has stumbled upon some very important information. Klefki has apparently been with Y's mother while she was held captive by Team Flare. If it also managed to get hold of Clemont's glasses, it could only mean one thing.

Without warning, X storms out from the tree hole, startling Marisso and Salame, and rushes back into Rhyhorn's tent to look for the map book. He soon finds the page which shows the exact same rock structures shown on Clemont's glasses, and realizes that Team Flare's hideout is at Geosenge Town.

Meanwhile, at Team Flare's headquarters, Clemont has regained consciousness inside the garbage incinerator chute. He uses his Aipom Arm to check on his surroundings via the chimney, and suddenly feels a rumble beneath him. Down in the underground chamber, Xerosic announces that the Absorber is about to be initiated, which shall begin charging up the Ultimate Weapon. Lysandre gazes upon the 'Tree', and declares that it is time to 'take' the bioenergy from Xerneas. At the same time, X has gathered his Pokémon together, and begins to make his way to Geosenge…