Xenial Destiny: Apocalypse: Rayquaza vs. Deoxys (Japanese: ゼニカル運命:黙示録:レックウザ対デオキシス Xenial Unmei: Apokaripusu: Rayquaza vs. Deoxys) is the seventh theatrical movie and the third Xenial Destiny series movie. It was released worldwide on January 22, 2016, set after Xenial Destiny: Apocalypse: Kyogre vs. Groudon.
With a meteor heading straight for Hoenn, Lexi and her friends are helping to try and do anything to stop it from arriving. Set once again to task by Steven, the group embark on yet another journey to stop the asteroid from hitting earth. But with Zinnia once again getting in their way, can they do just that? Or will Hoenn be destroyed by the oncoming calamity?
Mossdeep Space Center is shown before a warning siren sounds. A woman announces that a meteoroid is expected to make impact on "a small island southwest of Sootopolis, off of Route 131", presumably the Sky Pillar. Uncertain about the nature or origin of the meteoroid, which seems to be able to change its trajectory, they realise they must devise a plan to keep it from landing. Meanwhile, a Team Magma Grunt accompanied by a Whismur is shown standing atop the Sky Pillar changing out of her uniform and into a Draconid cape. She mentions that there isn't much time left, displaying knowledge of the meteoroid's existence, and thinks that "the stupid girl" may have complicated matters by not allowing the "super-ancient Pokémon" to undergo Primal Reversion. Regardless, she plans to make use of a Key Stone in order to revive Rayquaza, so it can destroy the meteoroid.
Elsewhere, Steve quickly takes a phonecall and tells Lexi he must leave, and before Lexi is able to ask him to stop, he vanishes. Marlon, Calem, Shauna, May and Brendan all gather around and ask what the thing in the sky is, which Lexi tells them she's unsure. Suddenly, the same woman from Sky Pillar turns up. She introduces herself and tells Lexi that she knows about her and her ability to use Mega Evolution. She comes up close to the group, and whispers something in Lexi's ear, which visibly shocks her, before she dashes off. Moments later, Lexi realises that she has stolen her Mega Necklace - angered, Lexi and the group are told by a bystander that they saw a girl and a Whismur flying on a Pokémon to Petalburg City.
In Petalburg City, Matt harasses Wally in front of his house. They are looking for a Key Stone as well. Suddenly, both of them are hit by an attack, knocking them to the group, before being ran passed by Zinnia. Moments later, Lexi and her friends fly down and ask them if they've seen a woman, in which they both tell them yes. Lexi asks Wally to borrow his Key Stone, however he reveals that his had been stolen, hence the issue with Matt. Matt tries to intervene but Marlon tells his Samurott to attack which sends Matt flying off. The group all wonder who this Zinnia is and why she's so adamant at being involved in Lexi's life. Shauna asks Lexi what she said, but she simply brushes it off. Luckily for her, her phone rings and its revealed to be Steven, who asks them to meet him at the Devon Corporation.
Steven meets the group outside of the Devon Corporation. He takes them upstairs to meet his father, who has a lengthy story to tell. He tells of a weapon created by one man to end a war 3,000 years ago in a distant region, a weapon powered by the life energy of Pokémon. Lexi is shocked and reveals her history with the Ultimate Weapon, demanding to know why he's telling her about this. He reveals that Devon developed that energy source into Infinity Energy. He then tells them about how they plan to avert the asteroid that is on a collision course with the planet by using a Devon rocket. To aid this plan, he asks that the group venture to Granite Cave and retrieve a Meteorite Shard, which is a key piece of their plan. He tells Steven to take the Link Cable he gave him and go to the Mossdeep Space Center and start preparations. Marlon agrees with Calem and Shauna that they will go help Steven, while Brendan and May will go with Lexi.
Once the group are at Granite Cave, they run into Zinnia and Aster (her Whismur) again, in a room with the wall painting. She reveals that this painting, showing Primal Reversion, was made by her ancestors, and alludes to another painting showing Mega Evolution. Turning away from the painting, Zinnia eagerly presses Lexi for a battle.
On the second floor of the Mossdeep Space Center, the group meet up with Professor Birch. He explains the plan to divert the meteoroid; which involves sending up a rocket and combining the Infinity Energy that powers it with human life energy like that found in Key Stones to recreate the massive energy used for Mega Evolution. This energy will be fired from the rocket to create a warp hole in the meteoroid's path, which will transport it somewhere far away.
In the middle of Professor Birch's explanation, an elderly woman appears to warn the group that using Infinity Energy means their plan will only repeat past mistakes. She hints as well at a new and greater atrocity that their plan will cause. She expresses disappointment that, with all of human knowledge and technology, they can't come up with a better plan. Professor Birch continues, and reasons with the woman, which she begrudgingly aceeps. He then explains that creating the warp hole will actually require a second, purer Meteorite Shard to the one Lexi will get, which can only be found at Meteor Falls. Hearing this, the woman reveals that if they're set on going through with this, she will show them where to find a purer shard, and so she and Steven head for Meteor Falls to meet Lexi.
Lexi and Zinnia continue battling before ending in a tie. Zinnia then gives her a Meteorite Shard, but before leaving, she pauses to question them about their motives and what they really know of the truth. Lexi is about to press for more when Steven shows up, and Zinnia disappears. Steven introduces the woman to Lexi, telling her that she is a descendant of the ancient Draconid people. The Draconid people are tasked with passing down the knowledge and story of Mega Evolution, which started with Rayquaza. The woman explains that, in the past, when a great disaster shook Hoenn, the Lorekeeper would offer up a wish to Rayquaza in front of a stone shining with rainbow light. In response to this wish, Rayquaza's body would become suffused with light and it would transform, gaining even greater power. She notes that later people would call this phenomenon "Mega Evolution".
The woman goes on to explain that the Lorekeeper is the person who has inherited the knowledge and power to summon Rayquaza if the world is again threatened. She then reveals that Zinnia is the current Lorekeeper, and that it was Zinnia who taught Team Magma & Team Aqua how to revive Groudon & Kyogre, planning to use that threat to summon Rayquaza so that she could then ask it to stop the meteoroid.
Steven is shocked that Zinnia would be involved in reviving the super-ancient Pokémon despite knowing the havoc they would wreak and the inevitable sacrifice it would cost. The woman contends that balance is the rule of the world and that even Steven's own solution must involve some sacrifice. She informs him that Zinnia will stick by her convictions to the end, even if it should mean sacrificing her own life.
Troubled by what they have learned, they all decide to head back to Devon.
When arriving back, a Scientist runs out, closely followed by a succession of both Team Magma and Team Aqua Grunts. They manage to ward them off, but the Scientist explains that they stole the control device for the Link Cable, a dimensional shifter. He believes they will head for the Mossdeep Space Center next.
Back at the Space Center, the group are awaiting the others to return while Courtney, Matt and a group of Grunts make their move on the Space Center.
Upon entering the Space Center, Lexi finds the visitors and employees clustered nervously in a corner opposite the group of Grunts who are blocking the stairs to the second floor. She and Steven battle them, and then they find find Courtney & Matt confronting the group upstairs.
Distraught that their leader's plans were foiled, Courtney & Matt decide they want to detonate the rocket, which contains even more power than the ultimate weapon in the war 3,000 years ago, destroying the world and thereby fulfilling Project AZOTH's goals. Not wanting this to happen, May and Brendan take charge and battle the pair. Once they are defeated, Aster shows up and snatches the dimensional shifter before Lexi has a chance to reclaim it. Zinnia then appears as well and claims that, while the dimensional shifter may indeed be their planet's best hope for being saved, it could also be an equally terrible tragedy for another planet. She tells of lore her people have passed down through the generations: that the mechanism of Mega Evolution also brings about distortions in the world, and that another world exists much like their own, yet also different. She suggests that in that other world, Mega Evolution is unknown, the war 3,000 years ago never happened, and the ultimate weapon was never built; and therefore, it would not have the technology to save itself if the asteroid appeared over it.
Unable to tolerate the chance that a helpless world might be put in danger just to save their own, Zinnia crushes the dimensional shifter. Steven and Professor Birch are dismayed at being robbed of their only hope, but Zinnia claims that she will be able to protect both worlds. Zinnia then rushes Courtney & Matt and steals their Key Stone. Before she leaves, Zinnia mentions that she already acquired Archie & Maxie's Key Stones. She then directly tells Lexi she hopes she will follow her to Sky Pillar, confusing the group, before leaving.
The group ask why she said what she had, and Steven reveals that only a Lorekeeper, those tasked with passing on the knowledge of the ancient world, can enter the Sky Pillar. He then reveals that Wallace is also a Lorekeeper and will know how to undo the Sky Pillar's seal. Steven decides to remain with the professor and his team to come up with a new plan to stop the meteoroid, leaving the task of stopping Zinnia to the group. He advises them to look for Wallace in the Cave of Origin at Sootopolis City.
Outside the Cave of Origin, having heard from Steven, Wallace explains that, as a descendant of the ancient people of Sootopolis, he can open the way to the Sky Pillar for the group. He also explains that the Sky Pillar is an altar built to Rayquaza, and that only the Draconids know how to summon Rayquaza. Wallace tells them he will help them to get to Sky Pillar, and they all head off.
They arrive at Sky Pillar, and Wallace undoes the seal. He tells them that they may proceed, but he is unable to accompany them inside himself. Instead, Wallace says he will return to Sootopolis and try to make his own contingency plans.
Just inside the entrance to the tower of the Sky Pillar, the group find Zinnia waiting for them. As they ascend the tower, she will tell the story of the Draconids' history, which is also enshrined in a mural covering the entire back wall of the tower.
Thousands of years ago, the world was overflowing with natural energy which Primal Groudon and Primal Kyogre constantly fought over, causing endless disaster for the people caught helpless in the face of their great power. Then, a storm of meteoroids fell upon a waterfall that a tribe of Dragon-type-Pokémon users had long called home. The meteors shone with a rainbow light, and, apparently in response to their light, Rayquaza descended from the heavens and quelled the pair of Primal Pokémon with its overwhelming power, bringing peace back to the world. The people of Hoenn took to revering Rayquaza as their savior.
A thousand years later, the meteoroids fell once again, and this time a huge meteoroid struck the planet and bore out the crater that would eventually become Sootopolis City. The impact cracked the lands, causing a great upswell of natural energy which once again woke Primal Kyogre and Primal Groudon, threatening further disasters. The people then prayed that Rayquaza would appear again to save them as it had before, and the huge meteorite that had bored out Sootopolis shone as if it were a huge Key Stone, and Rayquaza descended. In response to the people's wish for salvation and the light of the stone, Rayquaza underwent a change: Mega Evolution. Mega Rayquaza's Delta Stream subdued the power of the Primal Pokémon, and they returned to their dwelling places. A tall visitor from a distant land referred to Mega Rayquaza as the Δ (Delta) and said it was born of the world's disturbances and would calm them.
After this event, the Draconids built the Sky Pillar to hold the huge Key Stone that had granted Rayquaza its power, to bring themselves closer to Rayquaza's home in the sky, and to leave behind a record of their history and Rayquaza's might in murals.
Another thousand years of peace followed, but the Draconids predicted that the meteoroids would fall once more, and that the next time, there would be a meteoroid big enough to break the entire world. They devised a plan to prevent this calamity: they would find a way to call forth Rayquaza before the meteoroid struck and ask Rayquaza to destroy it.
This is the end of Zinnia's tale, and the group next find her on the top of the tower before the Dragonhark altar, gazing up at the night sky. She tells a brief personal story hinting at a loss in her past, before knocking them all out. Lexi awakes to find herself alone with Zinnia, who reveals she is ready to summon Rayquaza.
Zinnia offers herself before the altar and Rayquaza descends in response to her call. But when she asks Rayquaza to Mega Evolve, it cannot. Arriving at the conclusion that the Meteorites in Rayquaza's own body have lost too much power over the years, Zinnia despairs, until suddenly Lexi's Meteorite begins to glow like a Mega Stone. Rayquaza springs forth and swallows the Meteorite, giving it the power to Mega Evolve again. Zinnia then tells Lexi that Rayquaza wants to challenge them, and that they must win over Rayquaza.
They are heated in battle, which ends with Rayquaza calming down and offering itself to Lexi. Zinnia will teaches it Dragon Ascent, the move needed to get into space. Zinnia entrusts Lexi with destroying the approaching meteoroid. Lexi then rides Rayquaza out to space to destroy the meteoroid. They head their and find the meteoroid, which Rayquaza shatters easily, shocking Lexi. However, a triangular object emerges from the middle of the debris. After a moment of darting around, tendrils snake out of the object before it bursts apart to reveal the Mythical Pokémon Deoxys, who immediately engages them in battle.
After an intense battle, Lexi returns to the top of the Sky Pillar where Aster delivers a goodbye letter from Zinnia. The rest of the group return, before Wallace offers to escort them home. Back at the Space Center, the Space Center scientists are joyous at the meteoroid being destroyed; Professor Birch thankful to Lexi and the group as they return. They all head outside to watch the Litleonid meteor shower.
- Mid-Credits Scene
A man appears sat beside the sea, watching the sunset hit. A woman sits next to him, and lies her head on his shoulder. He smiles and kisses her forehead, before looking back into the sea. The lady gets a message, which she reads curiously before smiling. The man asks her why she's smiling, and she simply tells him "just you watch", before jumping up and running inside.
- Post-Credits Scene
A strange futuristic city is shown, with several robot looking people walking around. Suddenly, a cry is heard, and all the light from the city disappears. Several colourful gemlike shapes appear, with a growl being heard before the screen fades to black.