Reaching the shoreline where the Red and Blue Orbs are shown on the Scanner, Blaise and Amber come face to face with two men who appear to be their former leaders Maxie and Archie. However, something feels different about them, and the two former admins request to know who they are. Red and Blue are troubled that yet more people have shown up, and wonder if they are enemies or actually enemies of their enemy.

Suddenly, the entire area quakes tremendously, and the ancient titans Groudon and Kyogre roar to mark their arrival, much to the shock of Red and Blue but to the delight of Maxie and Archie. The two men are pleasantly surprised that Groudon and Kyogre have already awakened, and think they have shown up just in time. Blaise and Amber overhear Maxie and Archie address each other by name, and are bewildered that the men are really their former leaders. They are also flabbergasted by the strange appearance of the four Pokemon who are battling, since they strongly resemble Venusaur, Blastoise, Camerupt and Sharpedo, but at the same time look clearly different. Archie is disappointed that Amber doesn't know about Mega Evolution, and Maxie states that Blaise hasn't made good use of the past four years to enrich his knowledge.

Blaise and Amber gasp that the men know of their names, which means they are really who they appear to be. Archie remarks that he has a question of his own, and wants to know if they are the ones who summoned Groudon and Kyogre. Amber replies the affirmative, and Archie inquires about how they managed to awaken the creatures who are supposed to be slumbering in the Seafloor Cavern and the lava of Mt. Chimney. Furthermore, he wishes to learn of their purpose behind their actions. Amber quickly declares that he is doing it to resurrect Team Aqua and manifest their ideals, and explains that while they were searching for ways to reawake the titans, they have discovered the existence of a Pokemon named Hoopa, whose 'rings' can apparently link up different dimensions. Before Amber could elaborate further, Blaise stops him and says they shouldn't reveal everything to people with doubtful identities. Archie is amused that they are being referred to as suspicious, but Maxie doesn't really care and thinks Blaise and Amber has made their work easier, since all they need to do now is to verify the powers of the jewels.

With that, Maxie and Archie raise the Red and Blue Orbs towards Groudon and Kyogre, and the jewels glow intensely with the 'alpha' and 'omega' symbols. Red hollers that he wouldn't let them succeed, and orders Saur to snatch the artifacts with its vines. However, its attacks are blocked by Groudon and Kyogre, and Blue is astonished that the titans are protecting the men. Maxie and Archie climb aboard the titans, and grin that the creatures are also yearning for the powers of the Orbs, since they are the only means for them to reclaim their original powers. Amber gets baffled by their leaders' words, and Blaise realizes that the two men actually know what they are doing. Indeed, Maxie and Archie state that the jewels are more than what they appear to be, and Maxie knows that Blaise is already aware of the fact that they are not simply tools to control the titans.

Two thousand years ago, the Hoenn region was rich in a form of 'energy', which is perhaps best described as the 'natural energy'. Over the years, this pool of natural energy has slowly worn and dissipated, and not much of it is left as of today. Due to the dwindling of this energy, Groudon and Kyogre are no longer able to sustain their original appearance and powers. In the past, the two have fought endlessly, and it was no other than this energy that they were fighting over. Amber doesn't understand what they are implying, and Archie reveals that the Kyogre who sank half of Hoenn four years ago was actually in its suppressed state and didn't unleash its true powers. However, what's left of the natural energy has actually materialized in the form of jewels, which are the Red and Blue Orbs. By assimilating them, the titans could once again regain their original formes, not by powering up, but rather, reverting. With that, Maxie and Archie call upon Groudon and Kyogre to regain their former glory by undergoing Primal Reversion, and sink the Red and Blue Orbs into their bodies, which result in a blinding flash of light.

Meanwhile, Ruby and Emerald are still caught up in illusions, and find themselves surrounded by numerous rings, all of which have menacing eyes gazing upon them. Emerald frets that they will be in deep trouble if all the lurking creatures lash out at them, but Ruby soon realizes what they are dealing with and tells Emerald to keep his poise. Clearly, the Kindler whom they fought was no ordinary trainer but actually the former Team Magma Admin Blaise, who is an expert in wielding illusions by using the heat and flickering quality of flames. That said, the key to win is to find the culprit, and Ruby directs Latios to strike down the hiding Slugma, which instantly causes all the illusions to disappear.

Emerald marvels at Ruby's powerful mental strength, and Ruby grins that although he would really enjoy Emerald's words of praise, they should leave it to later. Right now, their priority is to head straight to the Meteor Falls, where they will hopefully learn something about Rayquaza. Emerald is shocked that they aren't going to do something about Groudon and Kyogre, but Ruby states that Rayquaza is the only Pokemon that could stop the titans, which means they must locate it in order to solve all of their current problems. Ruby gestures to Latios and Latias, and the two psychic dragons start speeding towards the Meteor Falls.

However, the boys soon realize that something is wrong, and Emerald states that the skies seem to have lightened up. Ruby finds it odd since it is still some time before sunrise, and soon spots what appears to be a cloud of energy quickly approaching. In the next instant, they are washed over by a powerful heat wave, and Emerald cringes in pain, hollering that the air burns as if it is a tsunami of steam. Ruby wonders if a meteor has landed, but Latios cries that it isn't and tells the boys to look ahead. To their shock and horror, Groudon and Kyogre materialize in the center of where the steam waves emanate from, but not only are they much bigger, their bodies have also changed in color and are giving off a strange menacing glow.

Latias states that they are unable to fly any closer, and Emerald wants to know why. Latias replies that it has no idea, but explains that it isn't ordinary heat wave that they are dealing with. Something strange is emanating from the two titans, and it is somehow repelling them off. Ruby and Emerald wear worried looks as they are kept at bay from the ancient creatures, and wonder what exactly is going on in the area.

Back on the shoreline where Red and Blue are, Saur and Blasty have successfully taken down Mega Sharpedo and Mega Camerupt. Maxie and Archie compliment the two for beating their Pokemon, and think they surely live up to their titles are the Kanto Pokedex Holders. The truth is, Red and Blue are literally under the weather, and the strange phenomenon in their area is giving them a hard time. Red wants to know how Blue is holding up, and Blue replies that the combination of heat, rainstorm and steam is taking a toll on her as well as Blasty.

Archie and Maxie state that with Primal Reversion, the titans' abilities have changed to Primordial Sea and Desolate Land, which is the reason why the current weather is in effect. They consider themselves fortunate that the titans have already been awakened, otherwise Red and Blue would have certainly defeated them and foiled their plan. Maxie grins that he really wishes to show his respect for their strength, but they couldn't afford to have them interfere with their goal. With that, he orders Primal Groudon to swallow them by the land, and the red titan immediately crumbles the ground beneath Red and Blue and sinks them underneath with Saur and Blasty. Blaise exclaims at the strength of Groudon's original powers, and Archie thinks he has found a way to test out Kyogre's. With his eyes on the S.S. Tidal, he gestures to Primal Kyogre, and the blue titan begins to create a powerful whirlpool, tearing the ship into pieces and sinking it along with those on board, Briney, Ultima and Drake, into the bottom of ocean.

Emerald cries that they need to save those on the ship, but Ruby stops him and states that they have a mission that has higher priority. With tears welling up in his eyes, Ruby states that their task is to protect the planet, and in order to achieve that they can only focus on one charge and cannot be distracted by other things. Emerald knows that Ruby is right but nevertheless feels himself torn and furious. Gritting his teeth in anger, he swears out loud, and fights to keep himself poised.

At the same time, Steven and his father Joseph Stone arrive at the Mossdeep Space Center on Metagross, and are astonished to see the massive crowd of media gathered outside the front door. Someone in the group soon spots their arrival, and the crowd immediately becomes unsettled, thinking that rumors about the asteroid must be true since the Devon Corporation funds the research of the Mossdeep Space Center. People start to shout out and ask why Joseph Stone has come and whether the asteroid is really going to hit their planet, but Steven tactfully bypasses the crowd and hovers directly into the building via the aerial route. He remarks that the situation is even worse than how Prof. Cozmo described, but Joseph Stone thinks it is only logical for people have such reactions. He hopes that he could pacify their worry by launching the rocket as soon as possible, and they are soon greeted by Cozmo and his assistants.

Joseph immediately asks about the Dimensional Shifter, and Cozmo replies that it has already been set in place. At that moment, Steven notices Sapphire, and is glad that she is safe. He hurries over to check on her, but discovers that she still hasn't regained her voice. The anxious assistant whose hair has two pointed tips says the girl hasn't eaten anything since she arrived the day before, and the jolly assistant who has three pointed hair tips thinks the food served at their food court doesn't fit her taste. However, the angry assistant with a single pointed tip in his hair believes it may not be as simple, and fears that she may have lost her sense of taste as well. Steven feels himself washed over by a sense of guilt as he recalls the emotional trauma he put Sapphire through, and yet the girl didn't pass blames at all and continued to treat him with respect and candidness. Although it was Ruby's idea to keep the secret from Sapphire, he couldn't deny the fact that he contributed to her pain.

Just then, Joseph Stone informs Steven that the rocket shall launch at 5am, and he will perform the final check with Prof. Cozmo. Steven checks his watch to see that it is 30 minutes later, and Sapphire taps Steven on his back to get his attention. She opens his palm and starts scribbling words on it with her finger, and Steven gasps with shock when Sapphire writes that Zinnia is just around. He inquires how she knows of it, and Sapphire explains by writing on his palm that she could sense her scent, breath and malice. Steven recalls having heard that when someone loses one of the five senses, be it sight, hearing, touch, smell or taste, the other senses will be heightened in order to compensate for the loss. For Sapphire, she has always had acute senses, and her loss of speech has clearly allowed her to be even more perceptive of the hostility, aggression and malice given off by Zinnia.

Sapphire begins writing on Steven's palm again, and Steven gasps when he reads that the girl is planning to strike proactively in order to fend off Zinnia. Without another word, Sapphire starts undressing, bewildering Steven and the assistants, and she reveals that she is wearing her leaf-suit underneath. Tossing away her shoes, head band, and rest of her garments, she starts smearing a dark Berry juice on her skin for camouflage. When she is done, she simply darts towards the cliff edge and leaps off from it, once again startling Steven and the three assistants.

Nearby, Zinnia stands on the tree branch of a mangrove, and sees that the rocket is about to launch. Behind her, Sapphire stealthily approaches, and before Zinnia could detect her presence, she slashes the tree branch Zinnia is standing on, and causes the woman to plummet. Zinnia catches a glimpse of Sapphire and her Gallade as she falls, and is astonished that she failed to sense them. She quickly sends out Salamence and Goodra to fight, and Sapphire calls forward her Aggron, Rono, to team up with Kirry. In no time, the four Pokemon lash out at one another, and start to engage in a close-up combat…