Upon arrival on the Hoenn coastline, the speedboat's autopilot system brings itself to a halt, and slowly anchors at the seashore. Archie and Maxie step off from the vessel, and the Team Magma leader states that the Red and Blue Orbs seem fully revitalized. The Team Aqua leader agrees, and points out that the 'omega' and 'alpha' markings can now be clearly seen. Coupled with the fact their shape and surface have also morphed, it is obvious that the jewels have filled themselves with a power even greater than before, which is probably in anticipation of their task in reverting certain beings to far more indomitable formes.

At that moment, two voices interrupt them, and wonder if the so called 'forme reversion' is the purpose behind the two men's actions. A boy in red cap who is flying on an Aerodactyl and a girl with brown long hair who sits on an inflated Jigglypuff show themselves, and state that although they have no idea what the term means, it couldn't be anything good if they had to injure someone and take the items by force. That said, they shall put a stop to whatever they are trying to do and reclaim the stones.

Archie and Maxie realize with amusement that the two young trainers have followed them all the way from Kanto, and the two introduce themselves as Red and Blue, Pokedex Holders of the Kanto region. The two men seem to linger on the phrase 'Dex Holder' upon hearing it, but Red and Blue give them no time to react, and promptly send out Blasty the Blastoise and Saur the Venusaur to fight. Archie and Maxie respond by calling forward Sharpedo and Camerupt, and the four Pokemon quickly engage in a close-up combat. Archie is surprised that Red and Blue have caught up with them so soon, and Maxie wants to know since when they have been aware of their activity. Red states that he is a close friend of Bill's, and reveals that it has actually been weeks since they discussed about the two stones.

Back then, Bill contacted Red via the visual phone system, and informed him of a mysterious phenomenon that was occurring to the red and blue stone plates. Bill felt as if the artifacts were gathering energy from their surroundings, and have even started to change in shape. Indeed, from the monitor screen, Red could see that the pieces no longer resembled the shards they used to be, but have grown bigger and more globular. Unfortunately, Red wasn't an expert in the field and couldn't really offer much advice on the matter. Bill reminded Red that the stones had a deep connection to Deoxys's forme change, and Red recalled the tough experience they had at the Sevii Islands. Normally, Deoxys could only access its Attack and Defense formes in Kanto, and the Normal and Speed formes in Hoenn. However, by using the two stone plates, which Team Rocket referred to as the 'Ruby' and 'Sapphire', Deoxys became able to morph into its Hoenn-exclusive formes at the islands, which suggested that the artifacts replicated the region's environment to some limited extent.

In their conversation, Bill has informed Red that the sisters in charge of the Hoenn Pokemon Storage System, Brigette and Lanette, have tried to investigate upon the roots of the items but to no avail. Nevertheless, they came to the conclusion that the stones were essentially the embodiment of Hoenn's natural energy, a theory that he actually agreed with. Now, with the artifacts rapidly drawing energy in and changing in appearance, Bill feared that something he couldn't handle on his own would happen and thus requested Red to pay him a visit. Red promptly agreed, and decided to ask Blue to come along since Green was currently not in Kanto. The next morning, together with Daisy, Red and Blue arrived at Lab Cape. However, to their horror, the whole place was a mess, and Bill lay injured on the ground with his left arm badly scorched. Apparently, the stones have been snatched by force, and the culprits also took away Bill's speedboat. After obtaining the speedboat's tracking device from Bill and placing him under Daisy's care, Red and Blue gave chase right away, which allowed them to catch up with Archie and Maxie as soon as they set foot in Hoenn.

Blue remarks that the incident has actually made it to the news, but was unfortunately overlooked by the public since everyone is far more concerned about the impending asteroid. As soon as Blue mentions the 'asteroid', Archie and Maxie begin to linger again, and their unusual reaction quickly makes Red and Blue suspicious if the two men might have something to do with the asteroid after all. Maxie states that he really hates to waste time, and Archie strongly agrees. With that, the Team Magma leader activates the Keystone embedded in the frame of the glasses, while the Team Aqua leader does the same to the anchor-shaped pendant he is wearing. In a flash of rainbow light, Sharpedo and Camerupt Mega Evolve, and the two men order them to give their best shot to celebrate the fact that they are finally back home after so many years.

Red and Blue are astonished that their opponents can wield Mega Evolution, and decide to do the same themselves. Raising their Keystones which are polished into finger-rings, Red and Blue call upon their light to intertwine with that of the Venusaurite and Blastoisinite, and morph Saur and Blasty into Mega Venusaur and Mega Blastoise.

Back on the shoreline near sea Route 115, Groudon and Kyogre fully emerge from the golden rings of Hoopa, and plunge into the waters with a big splash before resurfacing. Blaise and Amber rejoice that their plan has succeeded, and marvel at the greatness of the ancient titans. Blaise notices from the Scanner that the two Orbs have apparently returned back to Hoenn as well, and thinks everything is just perfect in timing. He truly hopes that it is their leaders who have brought back the jewels, and Amber gets thrilled that he may soon be able to see his former boss again.

On board the S.S. Tidal, Ruby and Emerald are still trying to digest the happenings in front of their eyes. Emerald wants to know if the titans are real and the same ones that Ruby fought 4 years ago, and Ruby thinks there couldn't be other possibilities since the beings are supposed to be one and unique. Emerald breaks into a rage, and yells at Hoopa for the mess that it has caused, which makes it drop its head in regret. Ruby says passing blames will not achieve anything, and suggests they come up with a way to deal with the two first. At that moment, Ultima, Drake and Briney return to the deck with Latios and Latias, and are bewildered to see the gigantic creatures. Ultima knows that they are the ancient titans spoken of in Hoenn's legends, and wants to know what exactly has happened. Emerald points a finger at Hoopa, but Ruby tells him to wait up and decides to check on his video camera's recording. He explains that Hoopa didn't summon the titans out of the blue, and shows everyone that the genie has actually been attacked while it was playing with Diancie. It then struggled with something on the other side of its ring which subsequently led it to drag out Groudon and Kyogre.

Drake can see that Hoopa summoned the titans because it wanted to overcome its foes, and Ultima wonders where this foe could be. Ruby points towards a nearby shoreline, and recalls seeing a momentary spark of flame when Hoopa began to attack through its ring. Since Hoopa's ring can bridge dimensions to reach faraway places, he believes that the enemy must be on the shore. Ultima wants to know if Ruby has any idea of who the foe might be, but Ruby states that he doesn't have a clue. Yet, it is apparently someone who knows of Hoopa's ability and deliberately provoked it to summon Groudon and Kyogre, which makes this person more than just an ordinary foe. Drake agrees with Ruby, and thinks they will have to bring down the enemy if they want to stop the titans. Latios gets an idea and gestures towards Diancie, and Ruby immediately realizes what it means. He climbs onto Latios with Diancie, and starts flying towards the ancient titans. As soon as he gets within a reasonable strike range, he asks for Diancie's help, and the jewel Pokemon starts to gather energy from the moon above. In the next instant, it fires off a powerful Moonblast, and manages to push back both Groudon and Kyogre. Ultima is completely astounded by Diancie's power, and Ruby believes that the pink little Pokemon has unleashed the move by converting and amplifying moonlight into energy waves.

At that moment, Briney spots two men and their Pokemon on the shoreline that Ruby identified, and Ruby hurriedly gets Latios to head over. Emerald decides to join him, and hops onto Latias who quickly speeds after Latios. Hoopa once again tags along, and continues to pull at Emerald's hair with its golden ring. In no time, Ruby and Emerald come face to face with Amber and Blaise, and call out Feefee and Dusclops to strike. However, Amber and Blaise are barely fazed, and comfortably fight back with Gorebyss and Slugma. While Gorebyss chokes Feefee with its slender body and subsequently slams it into the rocks, Slugma unleashes a barrage of fire balls which eventually overwhelms Dusclops. Ruby and Emerald are taken aback by the strength of their foe, and suddenly find Groudon and Kyogre right behind them. They quickly spin around to get into combative stances, but to their surprise, the titans simply move past them and continue on. The titans' behavior baffles the boys as well as the three adults on the S.S. Tidal, and Blaise snickers that they must think he and Amber are controlling the creatures. However, it is actually not the case, and the titans are simply returning to where the Orbs are.

Just then, multiple golden rings start to open up all around Ruby and Emerald, and each of them has a pair of menacing eyes staring out from the void, causing the boys to gasp and fret. Clearly, these are just an illusion created by Blaise's Slugma, but it succeeds in deterring the boys and giving Blaise and Amber a chance to slip away. Calling out his Swellow, Blaise goes airborne while Amber surfs on his Gorebyss, and the two stay close to the path taken by Groudon and Kyogre. Blaise thinks to himself that he shall scorch and incinerate the Orb bearer if it isn't Maxie. However, if it is indeed the Team Magma leader, they shall proceed to the next stage and revert the ancient titans back to their primal formes.

Soon, Amber and Blaise reach a shoreline where the Orbs appear on the Scanner, and lay eyes on two men, one in blue with the Team Aqua symbol on his headband and one in red with the Team Magma symbol on his collar. Yet, despite a strong resemblance to their former leaders, the two men also look drastically different, which make Amber and Blaise question who they really are.

Meanwhile, at the Meteor Falls, an elderly woman gazes upon the night skies via the hollow cave ceiling, and watches as the silhouette of a serpentine creature hover by. Suddenly, the three Draconids who attacked Ruby near the Sky Pillar come rushing to her with anxious looks, and she wants to know why they are so frantic. The three men inform her that some legendary Pokemon seem to have showed up near Route 115 to wreck havoc, and they wish to get to her permission to check out what is going on. However, the elderly woman answers by questioning if they have found Zinnia yet, and the men sheepishly reply that they haven't. The elderly woman states that those who couldn't fulfill their own tasks have no right to pass blames on Zinnia, and dispatch them back to their search. She then looks up once more, and gazes at the cloud lines in the sky, cloud lines that are left behind by their dragon lord…