The ending of Pokemon Legends Z-A is not very complex, although its events are directly related to a previous mainline title. Set in Kalos Region's Lumiose City and revolving around the Mega Evolution gimmick yet again, Legends Z-A explores the aftermath of Team Flare's actions with the Ultimate Weapon and also brings AZ's story to an end.
Although Team Flare is not up to their usual antics, Lumiose City faces a bigger threat that our protagonist and friends must avert, aided by Zygarde once again. This article explains the ending of Pokemon Legends Z-A, which also serves as a conclusion to the events of Pokemon X and Y.
Note: This article contains spoilers regarding the plot of Pokemon Legends Z-A. Proceed with caution.
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Pokemon Legends Z-A ending: Sins of the past come back to haunt Lumiose City
The story of Pokemon Legends Z-A revolves around three major stakeholders: the Prism Tower (or Ange), Zygarde, and AZ. The Prism Tower is situated at the heart of Lumiose City, and is managed by Quasartico Inc., a company that creates and manages Wild Zones to ensure people and Pokemon can stay together in Lumiose City.

If you have played Pokemon X and Y, you already know AZ, and Zygarde is the final legendary Pokemon of the Kalos region, one who maintains balance. During the opening acts of Legends Z-A, you will also meet Lysandre, the ex-leader of Team Flare, who is supposedly the voice of Zygarde and works together with the legendary monster.
Lysandre will inform you of ominous things that are about to happen to Lumiose City, and how the "3000-year-old man" will pay for his sins. Later, once you have progressed through the story and are near the ending missions, you ask AZ about the Prism Tower, he himself opens up and explains his backstory. AZ tells everyone present:
"Then I shall tell you of the terrible sins I have committed...and of my regrets."
AZ's story: 3000 years of lingering regret
3000 years ago, during the massive war that broke out, a lot of Pokemon lost their lives trying to settle the storm. AZ's own Floette was also sent to the frontlines, where she unfortunately lost her life. Unable to accept this outcome, AZ created a machine that could grant life itself. His idea was simple - use the machine to revive his Floette.

Although AZ had fulfilled his goal, his anger had not subsided. The countless number of Pokemon that lost their lives - AZ could not forgive the perpetrators. In a fit of rage, he modified the device and made it into the Ultimate Weapon, one that rained hellfire upon the earth and burned everything away. AZ explained:
"In my rage, I remade my device into the ultimate weapon. I put an end to the senseless conflict that would have taken everything from us. By becoming destruction itself."
AZ went on to explain what the ultimate weapon did:
"The light fired from the ultimate weapon reached the heavens, then poured down, burning away all that rested upon the earth."
On the other hand, the device that gave life to Floette also had its own secret - the life that it gave was actually 'stolen' from countless other Pokemon. Floette, possibly sensing this, left AZ's side, leaving him alone to wander for 3000 years.
The creation of Ange

Sometime during these 3000 years of lonely wandering, a great man requested AZ's help in protecting the Kalos region. AZ, still living in regret, decided to make a machine that would not take from others, but instead would grant eternal life, the same that he had given to Floette. AZ went on to say:
"At this, I thought to myself...I cannot make another device that would take from others. But perhaps I could make one that would share the eternal life that I had bestowed on Floette. That is what Ange is. That is what is hidden deep within Prism Tower."
According to AZ, his creating Ange was also a way of atonement, to reduce some of the burden that he had placed on his Floette by granting her eternal life. AZ eventually wanted to use Ange after reuniting with Floette.
Although this reunion did happen, Ange never got to see the light of day because the Pokemon world was living in a time of peace, with no real need for 'eternal life.'
Why Ange went berserk without Mega Floette at the helm

Now, it is clear so far that Ange was meant to be used with Mega Floette as its driving factor. To that extent, Ange should have remained dormant forever, without causing any trouble at all. However, the Rogue Mega Evolutions happening all across Lumiose City also seem to be caused by Ange, as surmised by AZ:
"But now Ange...The tower is emitting excessive amounts of Mega Power, even without Mega Floette present. This is only conjecture on my part, but I believe it may be related to the ultimate weapon being fired five years ago. That shock awoke Ange and has caused the Mega Power contained within it to spill forth."
This is where the story of Pokemon Legends Z-A starts to merge with Pokemon X and Y, and the former ends up becoming a direct sequel to the latter. We already know that Legends Z-A takes place five years after the events of X and Y, where the ultimate weapon was fired.
The ultimate weapon's use seems to have caused Ange to go berserk, and it now spills the Mega Power to forcibly cause Rogue Mega Evolution. Once again, AZ's creation that was meant to protect Kalos seems to have backfired into a weapon that causes problems for both the residents and Pokemon of Lumiose City.
The greatest Mega Evolution user

As Ange continues to swell up and leak more Mega Power, there's only one way to stop it according to AZ:
"A Mega Evolution user must Mega Evolve Floette and together reach the control panel within Ange."
Later that night, an explosion at the Prism Tower causes the structure to collapse partially, prompting Team MZ to rush to the location and proceed with calming Ange down. Your trainer and Taunie/Urbain will have a battle to decide who the greatest Mega Evolution user is, and the winner will Mega Evolve Floette in the control panel.
Despite you winning, it will be your rival who will take Floette to the control panel of Ange. The reason is simple - Zygarde only trusts the trainer, and must protect the city. Taunie or Urbain will Mega Evolve Floette, and the two of them will make their way to the control panel of Ange. Inside, Mega Floette supposedly uses her powers to calm Ange down, or at least it seemed that way.
Hyperrogue Ange Floette

The light from the Prism Tower dispersed as Mega Floette did her work. However, the light reappeared shortly, and the Prism Tower itself modified to become a mecha-biological structure, Hyperrogue Ange Floette. This structure was powerful enough to use Mega Floette's signature move Light of Ruin, and posed a serious threat to Lumiose City as a whole.
Just as Team MZ were at their wits' ends, Taunie/Urbain informs the others via the Roto Phone that they are safe inside the Prism Tower, and can spot Zygarde at a rooftop in the Magenta disctrict. The trainer makes their way to the legendary Pokemon, hoping to contain the calamity about to befall.

However, this travel is not going to be easy since the city is overrun by countless Rogue Mega Evolved Pokemon. All the top trainers of the city collectively come together to help, including Corbeau, Canari, Ivor and his sister, Jacinthe and Lebanne, and even Grisham and Griselle of Team Flare Noveau.
Complete Zygarde and Mega Zygarde

The trainer finally reaches Zygarde, who is still in its 10% forme. All Zygarde cells rush to the Pokemon, including the final cell that was on the trainer itself. Zygarde takes on its complete form and fights the towering Hyperrogue Ange Floette, while the trainer fights two flowers that the monstrosity spewed.
After the end of a rather tough battle, Zygarde Complete Form uses Core Enforcer to seemingly calm Ange down. The tower lost its movement and glow, and it seemed to be over finally. However, victory was short-lived as Ange's bud bloomed into a flower by breaking out of the shackles, and prepared to fire off one massive Light of Ruin attack.

At this point, the very uninteresting pebble that Zygarde had given you turns into a Zygardite, the Mega Stone for Zygarde, and you use it to Mega Evolve Zygarde instead. The supercharged Pokemon uses its new signature move, Nihil Light, to completely eradicate the Light of Ruin attack from Hypperrogue Ange Floette, and puts it back to sleep, once and for all.
End of the line for AZ
AZ, watching from the rooftop of Hotel AZ all this time, breathes a sigh of relief and bids his final goodbye:
"I will forever be grateful to you...Team MZ, my dear friends."
In the next cutscene, we see AZ's grave, surrounded by all the members of Team MZ. As the bittersweet moment passes, we also see L, or Lysandre, in the backdrop, looking at AZ's grave while saying:
"For three thousand long years, he bid farewell to so many...and now, we bid farewell to him."

Our protagonist spends just a few additional seconds looking at AZ's grave, which is adorned with flowers of all the Floette colors. Team MZ finally decides to head back and will continue to operate out of Hotel MZ, as a front to help and protect the people and Pokemon of Lumiose City.
With that, the main story of Pokemon Legends Z-A comes to an end. Zygarde is nowehere to be seen after the final battle, and Lysandre suspects the Pokemon is recovering its energy somewhere.
He also informs the trainer of the one that gives and the one that takes, referring to both Xerneas and Yveltal, the other two legendary Pokemon from the Kalos region. The trainer must now set out to capture these, and the additional story of Pokemon Legends Z-A continues.
For more articles on Pokemon Legends Z-A, check out the following:
- How to level up fast in Pokemon Legends Z-A
- How to get Hawlucha in Pokemon Legends Z-A
- Pokemon Legends Z-A: Best team for early, mid, and late game
- All returning Pokemon in Pokemon Legends Z-A DLC
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