Holding Courtney's memory fire lighter in hand, Ruby lifts his gaze towards the gigantic sky Pokémon Rayquaza. Although the dragon's entire body is continuously shrouded by ozone air which it breathes out from its mouth, when the ozone clears up occasionally, Ruby can clearly see his father, Norman, standing on top of its head, giving orders to the sky titan.

Ruby continues to read the messages stored in the fire lighter, and realizes that ever since their Rusturf Tunnel encounter, Courtney has yearned for them to become companions, and thus made extensive investigations upon him. Not only did she learn about his birth date, his age, his blood type, but also how he moved to Hoenn from Johto, the kind of family his grew up in, and the kind of childhood he had.

Among them, Courtney also uncovered things related to his father, Norman. She discovered that while the man has only become the Petalburg gymleader and moved in with his entire family from Johto recently, he has actually lost one gymleader selection test 5 years ago. The baffling thing lies in the fact that Norman has not attempted a second selection test within the 5 years, but has frequently visited the Mossdeep Space Center instead. The truth was, Norman was stripped of the right to sit for another gymleader selection test during the 5 years, and was ordered to search for Rayquaza.

Rayquaza is a legendary Pokémon that lives in the stratosphere between earth and space, whose activity was discovered and confirmed by the Mossdeep Space Center's observation data. Eventually, Norman found out that Rayquaza has left the stratosphere, and built its home atop the Sky Pillar. With knowledge that Rayquaza is the third ancient titan which has the ability to assert ordinance over Groudon and Kyogre, it was the Pokemon Association who bestowed the search mission upon Norman.

Ruby lets out a gasp when he learns that Rayquaza has the power to command the two other ancient titans, and realizes that together with the Red and Blue Orbs he possesses, he and his father, who has gained control over Rayquaza, are now the two people who hold all the keys to stop Groudon and Kyogre.

At that moment, Norman looks down from Rayquaza and meets the gaze of Ruby. Both of them know well the task that awaits them, and Norman has Rayquaza swoop down from the skies while Ruby hops onto its head to join his father.

Still with the fire lighter in hand, Ruby reads an additional message Courtney has inside, which speaks of a remark she made in the Rusturf Tunnel, the one which suggested Ruby become one of them and be their companion. Courtney now thinks that it was a redundant remark to make, because the truth is, she and Ruby have already been companions right from the start, both being fervent Pokémon contest participants. Stealing another glance at the crumbled Cave of Origin, Ruby silently voices his thanks to Courtney.

The boy then looks up to his father, who keeps his stare forward at Groudon and Kyogre without saying a single word. Ruby undersands well that his father prioritizes battling over everything, and agrees that they should leave all reunion talks to later.

As Rayquaza lurches itself towards Groudon and Kyogre, it wraps its long tail around the two and quickly immobilizes them. Ruby holds one orb in each hand, and with a determined look, dives down from Rayquaza's head, thrusting the Red Orb against Groudon's forehead and the Blue Orb against Kyogre's. The sky titan lets out its deafening roar of ordinance, and with the combined powers of the two mystical jewels, creates a powerful force which throws the land and sea titans away from each other.

While Ruby managed to land safely, Groudon and Kyogre keep tumbling back towards opposite directions, and soon fall off from the ascended ground of the Sootopolis City. Groudon crashes into the dried land below created by its drought ability and Kyogre plunges into the stormy seas it raged with its drizzle ability.

Both titans soon resurface with calmed looks on their faces, and after taking a final glance at Rayquaza hovering above, turn around to go their separate ways, Groudon digging its way back into the earth crust, and Kyogre sinking itself back into the deep seas.

On the Pokemon Association's giant airship, Ba.Goon, the Chairman, Captain Stern, Dock, the Pokemon Fan Club President, the Mt. Pyre old couple, Roxanne, Brawly, Wattson, Flannery and everyone else watch with disbelief at the monitor screen, and exclaim that the ancient titans, Groudon and Kyogre, have finally been calmed and are both returning to their respective places.

Back on the ascended ground of Sootopolis, Rayquaza allows Norman to dislodge, and Ruby feels glad that everything is over. He tells Norman that it is perhaps time he returns home and apologizes to his mom for leaving without notice, and hopes that the three of them will be able to spend quality with each other again.

However, Norman remains silent, and wears a blank look on his face. Ruby finds it odd that his father is not responding, and soon sees that something is very wrong when he notices the darkened eyes of the man.

Meanwhile, on the original eastern border Sootpolis, Wallace lets out a sigh of relief that the crisis is finally solved. Steven agrees with a grin, and says it seems that their task in holding down the two titans' destructive powers from expanding by Regirock, Regice and Registeel is now complete. But just as Wallace is about to respond, Steven suddenly topples over, and collapses on top of Registeel. Wallace gasps with horror, and frantically shakes Steven while calling out his name.

As Ruby does the same to his unresponsive father on the ascended ground, a low grumbling sound is heard from the direction of the Cave of Origin, and two pairs of evil eyes glare out from the darkness under the rubbles…

Thanks To Coronis For Writing this for us