At Geosenge Town, Y and the Gymleaders work hard with their Pokémon, and try their best to suppress the Ultimate Weapon from blooming. Nearby, Bryony hovers in midair by the propelling forces of her boots, and scoffs at how unsightly the Gymleaders are. She wishes that they would have thought of better ways than using brutal force to suppress the six 'Flower Petals' from opening, and finds it understandable why their Boss Lysandre doesn't regard the Gymleaders as chosen ones. One thing about the scene sparks her interest however. While it is logical for flying and psychic type Pokémon to stay suspended in the air, she wonders how ones like Avalugg and Tyrantrum manage to do so. She analyzes the scene with her visors, and soon realizes that the Gymleaders are using a tactic documented in Volume III's page 1048 and Volume VI's page 470.

Without hesitation, the green-haired Scientist sends out her Bisharp, and orders it to cut things through. Charging down from above, Bisharp delivers a slash with its blade-like arms, and manages to slice apart what appear to be invisible blocks in the air. Losing their ground, Valerie and her Mr. Mime plummet to the ground, along with Grant, his Tyrantrum and Aurorus, and Wulfric's Avalugg and Abomasnow. Wulfric hangs onto one of the opening 'Petals' which he continues to hold back, and asks to make sure that those who fell are alright. Bryony shows herself and giggles that they did use Mr. Mime to solidify air blocks and create standing ground after all, and Valerie is shocked that her trick has been discovered.

Ramos hovers on his Jumpluff, and believes that Bryony must be referring to the Pokémon Battle Encyclopedia when she mentioned the volumes and pages, which indicates that she is a keen reader. Bryony grins that Ramos must be a reader himself if he could make such a remark, and finds it a pity that he is a Gymleader. Ramos agrees that it seems they cannot be friends, and Bryony thinks it would be so mind fulfilling to talk about books if they had not been foes. Without another word, Bryony orders Bisharp to attack, and Ramos commands a Horn Leech from Gogoat to retaliate. The Coumarine Gymleader states that as someone who plants, he cannot be happier when flower blooms, especially when he witnesses the beauty of the petals open up little by little. However, the same cannot be said about this 'Flower' in front of his eyes, and it is the first time in more than 50 years of his gardening life that he encounters an ominous bloom. Bryony doesn't blame him since the flower last bloomed 3000 years ago, and Ramos argues that some flowers are not meant to bloom. Yet, Bryony disagrees, and says all flowers are made to blossom.

On the ground, Trevor feels nervous as he watches the 'Petals' of the Ultimate Weapon slowly open up despite their efforts to stop it. Suddenly, Shauna and Tierno whisper to him that they should get going, and Trevor wonders what they mean. He soon hears Olympia calling out to him, who urges him to remain stealthy as he hears her out. Trevor looks over to see that the Anistar Gymleader's eyes have turned hollow while her arms are stretched out, and knows that she must be wielding her psychic powers to suppress the bloom. Olympia reveals that the device that operates the Ultimate Weapon lies beneath the ground, which is also where Xerneas is, and wants the young ones to go under and find them while they work to hold back the 'Flower'. Trevor wonders if Olympia foresaw what is going to happen, but the Anistar Gymleader simply tells them to get going as she refocuses on channeling her psychic powers, which is clearly taking a toll on her body.

Tierno decides that they have no time to waste, and straps on his Roller Skates. He picks Shauna and Trevor up into his arms and starts to dash off, but their actions are quickly spotted by Bryony. The green-haired Scientist sees that the kids are heading towards the direction of the garbage furnace's chimney, and knows what they must be attempting to go underground via the chute. She states that no one can interfere with Boss Lysandre's work, and quickly retreats Bisharp from its fight with Gogoat. She sends it after the kids instead, and orders it to slash them into pieces. Distracted by their pursuer, Tierno trips on a rock just as he approaches the chimney and falls over. Bisharp quickly brings down its blade-like arm towards him, but right before it makes contact, something picks up the three Vaniville kids and pulls them into the chimney chute. The kids soon discover that they were saved by Clemont's Aipom Arm, and the Lumiose Gymleader, who is sitting inside the furnace, feels grateful that he caught them in time.

Trevor, Tierno and Shauna are glad to see that Clemont is safe, and Clemont expresses his shock that they have come to Geosenge. Trevor shows him the glasses he dropped, and explains how they figured out his location by its captured image. Clemont giggles that he really owes the Klefki and the Rhyhorn Racer Grace a big favour, but Shauna thinks they should be thanking Clemont for his marvelous inventions. She plops the glasses back onto the Lumiose Gymleader's nose bridge, and calls him Kalos's Master of Inventions.

Clemont then leads the three into Team Flare's Secret HQ via the corridor that connects to the garbage furnace, and Shauna wonders if Tierno and Trevor paid attention when the female Scientist talked about their Boss. Trevor feels a shiver down his spine as he heard Lysandre's name mentioned loud and clear, and Clemont confirms the fact that the man, who is a descendent of the Kalos royal family and also the person who invented the Holo Caster, is the leader of Team Flare. Truth be told, he himself still has a hard time believing it because like himself, Lysandre is also an engineer. The man has invested his own money to support research aimed towards trainers and Pokémon, and is generous person whom he genuinely respects. However, it turns out that he is also the Boss of Team Flare who took away the power from Lumiose City to power up the Ultimate Weapon in an attempt to destroy Kalos.

Tierno recalls that one of the Team Flare members once mentioned that their aim is to 'take' from the weak and 'give' to the strong in order to turn their world back into a beautiful place, and Shauna scoffs that the term 'beautiful world' sounds ironic with what they are doing. A voice comes on to explain that it is a 'beautiful world' by Lysandre's idea of balance, and Shauna tells Tierno not to speak with such a weird tone. However, Tierno protests that he didn't say anything, and the voice goes on to say that Lysandre is seeking to create a world where the residents, Pokémon and essentially everything of Kalos cease to exist.

Clemont, Trevor, Tierno and Shauna turn around towards the source of the voice, and are bewildered to see a giant man with long white hair held captive inside a cell. Frightened by the man's appearance, Shauna stutters and wants to know if he is human. At that moment, Emma shows herself with Mimi, and introduces the man as AZ. Shauna recognizes Emma as one of Cassius's assistants, and the girl slips out from the cell between the metal bars, explaining that she and AZ just became friends.

When Trevor would think back on the first time he saw AZ, who was clearly taller than 3 meters, he would always remember how the man strangely reminded him of Lysandre. However, unlike Lysandre, the man didn't horrify him, and neither did he appear mysterious.

AZ spots Trevor's Flabébé, and wants to know if it is his Pokémon. Trevor responds with a nod, and the giant man gently touches the little flower fairy, admiring its beauty. He inquires about the Ultimate Weapon, and Trevor is shocked that he knows about it. AZ says he has no time to explain in detail, but they must stop Lysandre at all cost because everything will be lost if he manages to unleash the beams of destruction from the weapon. Trevor feels alarmed by AZ's words, and is desperate to know what they should do since the flower-like structure is about to bloom and the Gymleaders are doing everything they can with their Pokémon to suppress it. AZ feels bewildered that the weapon is already blooming, and knows that Lysandre must have used the Key. After a moment of thought, he states that they still have time before the 'Flower' fully blossoms, and Emma believes that they must work to reclaim the Key.

Trevor wonders what the Key means, and Emma explains that Team Flare took away a Key from AZ which is the item needed to activate the Ultimate Weapon. AZ states that they may still stop the weapon if they manage to pull out the Key before it fully blooms, and the kids realize that they really have no time to waste. Tierno thinks it would help if AZ comes with them, and gets Corphish to break the bars with a Guillotine. Shauna is glad that the move it learnt from Gurkinn's training was put to good use, and Emma helps AZ get back onto his feet since his legs must be numb after having crouched inside the small cell for so long.

As AZ leads the kids to where they should go, he shares with them a tale which took place a terribly long time ago…

'There was a man and a Pokémon. He loved that Pokémon very much. A war began. The man's beloved Pokémon took part in the war. Several years passed. He was given a tiny box. The man wanted to bring the Pokémon back, no matter what it took. The man built a machine to give it life. He brought his beloved Pokémon back. The man had suffered too much. His rage had not subsided. He could not forgive the world that had hurt the Pokémon he loved. He turned the machine into the ultimate weapon. The man became a bringer of destruction that ended the war. The Pokémon that was given life must have known… that the lives of many Pokémon were taken to restore its life. The resurrected Pokémon left the man…"

Having listened to the tale, Trevor wants to know who the man in the tale is, but AZ says they have arrived at their destination, and proceeds to open a giant red door which has Team Flare's logo on it. Upon entry, the Vaniville kids gasp in shock, as they see X lay unconscious on the ground next to Kanga, Li'l Kanga, Elec and Lasma. They then spot Xerneas has reverted to its true forme, but it standing motionless in the middle of the room. Trevor thinks it looks different from the time they saw it in Vaniville, and points out that its antlers are now blue.

Suddenly, the group finds themselves surrounded by a Mienfoo, Pyroar and Gyarados, and Tierno recognizes that it is the team party of Lysandre. Trevor notices that Gyarados has taken on an alternate appearance, gaining a bulkier body and much bigger side fins, and postulates that it must have Mega Evolved. Clemont wonders where the Key is, and AZ quickly points towards the small platform suspended in midair, where Lysandre is still standing on in his cybernetic suit.

The sight of Lysandre causes Trevor to tremble and drop to his knees, but despite his terror, he also feels rage. Speaking with a stuttering voice, he states that they must pull out the Key immediately. Shauna protests that they should help X first, but to her shock, Trevor snaps at her and cries that she is wrong. He hollers that it is more important to pull out the Key than to save X, and requests Clemont to help him get onto the platform. Clemont quickly hoists Trevor onto the platform with his Aipom Arm, and the orange-haired boy finds himself face to face with the man who greatly terrifies him. However, he fights back his fear, and demands the man to remove the Key. Lysandre grins that Trevor is also a chosen one, and taunts him to his own strength to defeat him and retrieve the Key himself. Trevor furiously states that he chooses not to be a chosen one, and bends forward without warning, causing the flap on his backpack to open. Inside, Flabébé takes aim, and fires off a powerful Solar Beam to knock Lysandre off the platform.

Tierno and Shauna exclaim and applaud at their companion's good work, and ask Clemont to help them onto the platform as well. The Lumiose Gymleader lifts the two up with his Aipom Arm like he did with Trevor, and the three Vaniville kids begin to pull at the imbedded Key. Above ground, Y and the Gymleaders clench their teeth, and continue their struggle in holding back the 'Petals'.

Alas, their combined efforts fail.

With a loud bang, the Ultimate Weapon blooms to its fullness, and unleashes a powerful explosion of light, its waves reaching to all the surrounding towns and cities, knocking down lampposts, toppling trains and even washing sailboats offshore.

AZ gazes up with a look of hopelessness on his face, and mutters that they failed to stop the weapon in time after all. The lights of ruin have swept the entire Kalos just like before, causing everything to vanish and bringing an un-ending pain once again. However, Xerneas speaks out telepathically at that moment, and says it disagrees. It points out that the one thing is different from 3000 years ago. Right here, there are humans, and one of them shall hold it inside a Pokéball…