Prologue/Backstory:
Some information about this fanfic. I am writing this while the Pokémon XY&Z series is going on and the Mega Evolution Special has already aired its final and fourth episode, so we don't have any information on how Ash/Satoshi and the gang will meet with Alan/Alain and Team Flare/the Flare Gang and what will be going down with Zygarde, or even how the inevitable Complete Form Zygarde will play a role in all of this. So here is my head canon/fan theory to give a little back story for this fan fiction (I'll be using the Japanese names). This also occurs after the first episode of the Pokémon XY&Z series:
Alan is working for Fleur-de-lis thinking that he is aiding in the establishment of a Mega Evolution energy system, not only to help Manon's Harimaron, Hari-san, get better, but to help the world through peaceful means. Little does he know that he is actually working for Team Flare to further advance the making of the Ultimate Weapon and the destruction of the whole world.
Satoshi and gang arrive at Terminus Cave to find Team Flare members sneaking about, trying to catch Zygarde 50% (Z2), and realize what Puni-chan (Eureka's name for the Zygarde Core) really is. After stopping Momiji and Akebi from capturing Z2, Satoshi and gang find out about Team Flare's plan to 'create a beautiful world,' but with no more details on their grand scheme, they continue on their way to challenge the final gym for Satoshi's last badge.
After the Team Flare Scientists Correa and Bara fail to capture the Zygarde Core (Z1) from Satoshi and the gang multiple times, Alan is sent to stop them and take it back to Fleur-de-lis, under the guise that the Core is key in harnessing the power of the megalith. Thinking that Alan is working for Team Flare, they tell Alan of the Team's schemes and refuse to turn over Puni-chan. However, Alan knows nothing about a "Team Flare" and is adamant that the Core is used to find a source of energy in order to heal his friend's Harimaron, and that the director he is working for is working towards a more peaceful future. After escaping from Alan, Satoshi and the gang continue on their way, but a seed of doubt is planted into Alan's head. Confronting Fleur-de-lis about who Team Flare is, Fleur-de-lis reveals that he is head of the team, thus confirming Alan and Satoshi's suspicions that Puni-chan would not be used for good and peace, but for a much more devastating cause; no matter how Fleur-de-lis sugarcoats it, the beautiful world he pictured would only be brought about by the destruction of man and Pokémon.
However, because Harimaron and Manon are being taken care of at Fleur-de-lis Foundation, Fleur-de-lis has leverage over Alan to make him continue in helping bring back the Zygarde Core to the labs. Faced with no choice, but with more information about what he is getting himself into, Alan searches for Satoshi and the gang again.
After Correa and Bara hear that Alan now knows of Team Flare's plans, they plan to get rid of him, in case Alan has a change of heart. After Alan finds Satoshi again, he finds that he needs to trust in the others because they hold a vital key in stopping, or at least hindering, Fleur-de-lis' plans. Correa and Bara attack Alan and the others, thinking to kill two birds with one stone, getting rid of Alan and recapturing the Zygarde Core. Alan brings out Lizardon and mega evolves him, much to the surprise of Satoshi and the gang, however, Correa and Bara have predicted this and use a device that not only prevents stops the mega evolution, but cripples Lizardon horribly. Satoshi and the others try to fend off Correa and Bara's Pokémon, but the Team Flare reinforcements prove too much for the kids. At this moment, Puni-chan summons Zygarde Cells and transforms into Zygarde 10%, unleashing a powerful earthquake. Finding that the newer form of Z to be too powerful, Team Flare retreats. Alan recognizes the green glow of power to be similar to the one that envelopes Manon's Hari-san, and believes that Puni-chan is somehow connected to the comatose Harimaron. After giving them a short version of what has transpired, Satoshi and the gang agree to help Alan try to cure Hari-san, and though it may be dangerous, head to the Fleur-de-lis Foundation.
The party manages to sneak onto the grounds and find their way to the room Hari-san is being treated in. Alan sees Manon inside, staring dejectedly at Hari-san. Feeling sorry, Alan enters the room first, thinking to talk to Manon about what he had said when they previously saw each other. Even though Manon is hurt, she forgives him and is just happy to see him again. Alan then begins to tell Manon that he may have found a way to cure Hari-san. At this, Satoshi and the others come into the room. After introductions, Eureka brings out Puni-chan. Puni-chan recognizes Hari-san as the Harimaron that had helped it escape from the lab, and after making contact with the comatose Harimaron, Hari-san wakes up. Everyone is ecstatic at Hari-san's awakening and even Alan is relieved to have found a cure; no longer trusting Fleur-de-lis, he tells Manon that they need to quickly get out of the Fleur-de-lis Foundation.
However, before they could do so, the director of the foundation himself enters the room and seizes Puni-chan, saying that although Hari-san had woken up, thus making Manon and Hari-san unusable as leverage, Alan was still useful in helping him retrieve Z1, the last piece of the puzzle. The party makes a mad dash to follow Fleur-de-lis and Puni-chan, however, it was too late and Puni-chan had begun to be subjected to the cruel tests and lasers it had previously escaped from. This time, Satoshi, Alan, and the others could do nothing but watch as Puni-chan's powers were used to power the megalith, the ancient weapon used in a war 3000 years ago and would be used again to create a beautiful world. There is little to do except hold on to each other as the Ultimate Weapon charges itself.
This pending disaster leaves no other choice than for Puni-chan to summon all of its cells, transforming into its complete, 100% form. Though Fleur-de-lis had a plan to try to capture this power, it proved too great to contain, and the ancient weapon and lab were destroyed. Still sensing some imbalance, Zygarde set on an uncontrollable rampage. No longer the protector of the Kalos region, it seemed as if it was the combination of destruction and life, containing the powers of both the legendaries Xerneas and Yvetal; seeing the horrible acts of Team Flare may have convinced Zygarde to make the Kalos region or even the world anew. By working together, Satoshi and Alan were able to challenge Zygarde Complete Form's power, but it was Eureka's determination and want to bring Puni-chan back that stopped Zygarde's rampaging and transformation back into the Zygarde Core. Even though the Team Flare was no more, Fleur-de-lis and his scientists were nowhere to be found, though the Kalos Police assured the kids that they would still be searching for those who had escaped. With the ordeal over, Alan and Manon decide to return to Professor Platane's Laboratory in Lumiose City to rest while Satoshi and the others continue on their journey.
However, even with everything resolved, Alan still felt the guilt of having dragged Manon into such a dangerous situation and vowed that even though he may be strong enough to protect those he cares about, being with him was just too dangerous. Thus, Alan decided to leave Manon to set out on a journey across Kalos alone. Professor Platane, along with the Kalos Police, had managed to recover some data from the Fleur-de-lis Foundation on mega stones and mega evolution, and even though he didn't approve of Alan setting off alone without at least saying goodbye to Manon, he understood Alan's conviction and blessed him a safe journey, with the promise that every discover Alan made would be reported back to him.
It has been six years since the day Alan left the Lumiose City Laboratory, and with Alan's help, Professor Platane's breakthrough discoveries on mega evolution have changed the world over the past few years. Today is the first time in six years Alan has returned back to Lumiose, after being persuaded by Professor Platane to come and enjoy the annual summer fair Lumiose holds to celebrate trainers who have entered the Kalos Pokémon League and fought against the Elite Four and the Champion of the Kalos region.
Though anxious at being back in Lumiose, today is just another day for Alan, and even though he feels guilty about the past, he also looks at what could be seen in the future. But even though he has been traveling for six years, Alan is still uncertain about what could be seen past the horizon. What awaits Alan on the dawn of a new day? Just a day at the Lumiose fair, or something more?
