After stepping through Hoopa's ring, Ruby and Norman find themselves transported to the front of the Pokémon Association's laboratory in the Johto region. As they approach the destroyed building, Ruby senses that his father is angry with him. He correctly assumes it is because he kept his plan to destroy the meteor a secret, and hurt his loved ones because of it.
To get inside the laboratory, Norman has his Sawsbuck use Horn Leech on the wood panels blocking the entrance. As they enter, Norman tells Ruby that the laboratory is owned by the Berlitz Family, and that the Devon Corporation had supplied them with the technology. Norman unlocks a storage room with a key, then locates the records of Rayquaza's capture on a computer as Ruby finds a shred of fabric that looks similar to the pattern worn by the Draconid people. Norman calls Ruby over to the computer, where a video is playing on the screen.
In the video, Mr. Stone is documenting the plan to capture Rayquaza at the Embedded Tower. He shows off a device that he calls the "Flower," which works by taking in Rayquaza's life force. Rayquaza soon appears, attacking everyone around it. Watching the footage, Ruby notices a figure riding on the back of Rayquaza and alerts his father. He realizes that it is the former Lorekeeper, who proceeds to Mega Evolve Rayquaza with a Key Stone. The video suddenly cuts short, and Ruby and Norman debrief what they saw. Recalling that Rayquaza ended up being captured by the Pokémon Association, Ruby wonders what happened to the person riding it. He thinks of Zinnia and her hatred of the Devon Corporation.
Norman realizes that Rayquaza may have gone to the Embedded Tower on Route 47 instead of the laboratory like he and Ruby had thought. They make a plan to head over there, but Norman stops to reveal that Emerald has given him the Green Orb. Norman places it inside a machine, and it begins to change color, surprising them. Suddenly, the room begins to shake. Parts of the ceiling begin to crumble, and Ruby and Norman sprint out of the building. Outside, they look up to see meteorites falling from the sky. To their shock, one of the meteorites is crushed between the large jaws of a Pokémon—Rayquaza.
The two hop onto Norman's Staraptor's back and chase after Rayquaza. They try to get its attention, but it is only focused on eating meteorites. Ruby sends out Fofo and commands it to use Sunny Day, drawing Rayquaza's focus onto them. They fly close to it, but Rayquaza grabs Ruby in its claws. As Norman desperately attacks Rayquaza, Ruby pulls out the Draconid people's scroll. The letters on the scroll begin to disappear, the ink dissolving off of the page. As Ruby is squeezed tight in Rayquaza's grip, he tells Norman to get Emerald to warp them all to Hoenn with Hoopa's rings. Ruby explains that they will focus on befriending Rayquaza when they get back, and that he intends to destroy the meteor with Sapphire.
