It is the early morning hours of the day. In a deserted area, a mysterious golden ring slowly materializes in midair, and Ruby soon appears within it along with his father Norman. The two proceed to step out from the ring, and see that they have indeed made it to the Johto region. It would appear that the traveller's thoughts can really dictate where Hoopa's rings connect to after all, and right now, they are at the former site where Pokemon Association used to several of their facilities.

Ruby looks around, and soon spots the arena where his father underwent the Gymleader selection test years ago. Adjacent to it, he recognizes the bushes where Zinnia's Salamence attacked them, and further down the road, there is the Research Building which used to hold Rayquaza captive. From the wrecked state of the site, it is clear that no restoration has been attempted since it was destroyed, and Ruby is really curious as to why the Pokemon Association abandoned the place, essentially turning it to a ruin. Before he could raise the question however, he sees his father heading off towards the Research Building without a word. Although it has been some time since he saw it, it is no doubt a demeanor of anger.

Ruby believes that Norman is upset at him because he acted in secrecy about the giant asteroid, but on another thought, thinks it may also be due to his decision to embark on Rayquaza to destroy the asteroid. It doesn't take long for his query to be answered, as Norman speaks up at that moment, and says Ruby's mother is extremely worried about him. Ruby immediately cringes at the remark, realizing where his father's anger came from, and Norman states that he will not pass blames on Ruby for the way he handled the asteroid matter. However, he hopes that Ruby can keep in mind that his reckless actions will cause those who care for him to suffer, and the boy acknowledges his father's words with a solemn look.

Arriving at the front door of the Research Building, Ruby sees that it is sealed by rows of wooden planks, and Norman explains that the facility has been abandoned and blocked from access since the incident 9 years ago. After all, if the Pokemon Association simply pretends that the whole thing never happened, they would not have to deal with the mistakes they have made in the past. The Petalburg Gymleader sends out his Sawsbuck, which has taken on the Winter Form, and commands it to slam down the sealed door with a Horn Leech. He then steps into the building, and Ruby wonders if it is alright that they break in like that. Norman reveals that he has gained permission from the proprietor, and says the facility is actually under the ownership of the Berlitz family from the region of Sinnoh. Ruby wears a look of confusion upon hearing the name, and Norman explains that the Berlitz family is a wealthy clan which has produced many Pokemon scholars throughout the generations. Years ago, when the Pokemon Association proposed the 'Rayquaza Capture Project', the family agreed to provide financial support on the condition that they get to participate in the research. The project also received technical support from the Devon Corporation as well as a company known as the Greater Mauville Holdings which apparently no longer exists. Ruby is astonished that Devon was also involved, and Norman remarks with a snicker that they were only interested in the legendary Pokemon's power and energy.

The father and son soon find the entrance to the storage room, and Norman states that according to Yanase Berlitz, it still holds certain data files pertaining to Rayquaza's capture. Yanase has said that if the emergency power supply has run out, they could tear down the door locks by force, but it seems that luck is on their side, and the electronic key she gave him still works. With that, Norman and Ruby gain access to the storage room, and Norman starts searching for the data files on the old computer. While his father is occupied, Ruby scans the room, and sees a row of glass jars containing different artifacts. One of them catches his attention, and upon a closer look, he sees with astonishment that it is a piece of garment which bears the Draconids' symbol. The garment's charred edge suggests that it has been burnt, and the more he looks at it, the more he feels that it was part of the torn cape that Zinnia wears.

Just then, Norman successfully locates the file, which is actually a video recording. He starts playing the clip, and a strange looking cliff side with a cave opening lined with symbols appears on screen, which Norman recognizes at the Embedded Tower, a ruin located on Route 47. The camera spans to a familiar looking man who stated that the process to capture Rayquaza shall begin, and Ruby gasps that it is President Joseph Stone in his younger days. Behind him, a team of fully-equipped men are seen with several Ampharoses and Sneasels, and Joseph Stone remarked that they shall use their special device known as the 'Flower' during capture, which could immobilize the target with the help of Infinity Energy. By zapping away Rayquaza's bioenergy, its capturing process would be much easier. However, before Joseph Stone could finish his sentence, his men began to cry out in horror, and in the next instant, the camera shows Rayquaza appearing and attacking the team. Joseph hollered that they should activate the 'Flower' immediately, and at that moment, Ruby spots something and tells his father to pause the clip. He zooms in to Rayquaza's head, and although it is blurred by the ozone continuously breathed out by the dragon, there is undoubtedly the silhouette of a person atop the legendary Pokemon.

Norman resumes playing the recording, and the 'Flower' device was soon ready to fire. In that instant, the human silhouette on top of Rayquaza activates something to give off a rainbow-coloured light, and Rayquaza begins to morph into a different forme, sporting a longer, leaner body with numerous tendrils extending from it. Due to the blinding flash, Ruby and Norman could only see the outline of the dragon's new appearance, but it is shocking enough for both of them. Unfortunately, the video ends at that point, and gives no further clue on what happened next.

Norman postulates that Rayquaza must have either undergone Primal Reversion or Mega Evolution, and Ruby is inclined to believe that it was Mega Evolution. When the rainbow coloured light flashed in the clip, he could faintly see the person crouching down to activate something on his or her ankle, which he has seen Zinnia do the same with her Mega Anklet when she Mega Evolved Salamence. He then shows the jar containing the burnt garment to his father, and says the piece actually made him unsettled. They all know that Rayquaza ended up being caught although the video didn't show it, which makes him wonder about the fate of the person riding on it. He recalls Tomatoma saying that everything has been taken away from the Draconids and how Zinnia declared Devon as her enemy, and couldn't fight the thought that this is all connected.

Meanwhile, Norman has something else on his mind, and after a moment of contemplation, voices out his worry that they may have made a wrong guess about Rayquaza's intended destination in Johto. Ruby wonders what he means, and Norma explains that since they now know the Embedded Tower is Rayquaza's habitat in Johto, it is perhaps the Embedded Tower that the dragon was headed instead of this research facility. Ruby thinks Norman is probably correct, and suggests they head to Route 47 right away. However, Norman says he actually came to the facility for one other purpose, and takes out the Green Orb, which he borrowed from Emerald before they entered Hoopa's ring. The man explains that the artifact was developed by the Pokemon Association in an attempt to control Rayquaza. Unfortunately, Rayquaza broke out and escaped before its completion, and according to Yanase Berlitz, if they manage to further heighten its purity, it would reach completion and change its colour to a shade of jade. Hoping to give it a try, Norman places the Green Orb into the purification device and activates the machine. Indeed, as the artificial jewel gets further engineered, its colour slowly starts to change.

Suddenly, a loud rumble shakes the entire building, and causes rubbles to fall from its already broken ceiling. Ruby and Norman hurry out to see what is going on, and are bewildered to spot a shower of the smaller asteroids falling from the sky. Ruby is shocked that they have started to affect Johto as well, and at that moment, a giant serpentine creature materializes from the clouds and catches a few asteroids in its mouth. The father and son gasp that it is Rayquaza, and are astonished to see it devouring the rocks from space. Ruby checks on his Pokedex, and discovers that Rayquaza indeed feeds on meteoroids.

Norman thinks Rayquaza appeared at the perfect timing since it saves them the trouble of going to the Embedded Tower, and tells Ruby to get the scroll ready. The Petalburg Gymleader then calls out his Staraptor, and goes airborne on it with his son to chase after Rayquaza. Soon enough, they make it to the legendary Pokemon's side, but the sky dragon is completely oblivious to their presence and simply has its eyes set on the falling meteoroids. Norman says they will need to get its attention, and Ruby proceeds to send out his Castform, Fofo. He orders it to unleash a Sunny Day, which casts a strong light on Rayquaza, forcing it to close its eyes. In that instant, another small asteroid falls from above, and hits Rayquaza on its back, knocking it off its flight. Norman hollers that it is their chance and swoops down with Staraptor. However, the sky dragon manages to halt its fall, and somersaults back up, snatching Ruby off into its claws as it regains altitude. Norman cries out after his son, and angrily demands Rayquaza let go of him. He gets Staraptor to attack with a Final Gambit, but the dragon easily blocks it with its tail.

Wincing in agony, Ruby tells Norman to hold up, and starts to unfurl the scroll. The ancient symbols on the scroll appear to catch Rayquaza's interest, and Ruby is glad that he has its attention. He believes that Rayquaza also wishes to acquire the move in order to express its true powers, and as soon as he says that, the ancient writing on the scroll flashes intently and begins to detach into thin air. In no time, the scroll becomes blank, and Ruby wonders if it has achieved its purpose.

Just then, Rayquaza tightens its grip on Ruby, and causes him to grunt in pain. Norman desperately holds up the supposedly purified and functional Green Orb, and demands that Rayquaza succumb to his command. However, it doesn't seem to affect the dragon as he has hoped, and Ruby asks his father to contact Emerald right away and get Hoopa to summon them back to Hoenn along with Rayquaza. He thinks befriending Rayquaza will have to wait, and says the giant asteroid is heading straight for a solitary island on the water Route 131 according to Steven. Although it may be difficult, it is his hope that he will take on the asteroid above the solitary island together with Sapphire…