At the Battle Frontier, a giant monster created out of sea water, resembling the appearance of the ancient titan Kyogre, looms over the entire island as dark clouds shroud across the evening skies. At the top floor of the Battle Tower, Guile Hideout gets back onto his feet with the help of his sword, and wants to know if Gold just said the ceremony is about to begin.

Gold puts on a look of disdain as he rests his billiard cue over his shoulders, and says he hates to repeat himself. He hopes the armoured man will listen more carefully and clear his ears first, but wonders if his armour is preventing himself from digging out his earwax. Guile Hideout shudders with rage at Gold's tone of mockery, and holds his fists in anger as he and his Surskit glare at the boy.

Gold turns around to face Ruby, Sapphire and Emerald, addressing them as the fashionable lad, wildchild girl and unorthodox boy, and properly introduces himself as Gold from New Bark Town, while the ultra serious girl next to him is Crystal, a description that causes Crys to frown with annoyance. Gold declares that they have come to reverse their seniors as well as his good ol' pal Silver from their petrifaction, and with that, propels himself forward with the help of Aitaro's bouncy paw-like tail and swings his billiard cue onto Guile Hideout. Unfortunately, the armoured man fends off the strike timely with his sword, and delivers a swipe to send Gold tumbling backwards.

Ruby gasps in bewilderment as he takes a look at the five statues in the room, realizing that these stone blocks of the senior Dex Holders are not just for decoration purposes. Sapphire finds it hard to believe that the statues are in fact petrified humans, but Gold reiterates that what he said was nothing but the truth. Emerald turns to Crys with an astounded look, but Crys simply nods to acknowledge Gold's claim.

Guile Hideout holds up his sword and prepares to deliver another attack, and Gold quickly tells everyone to gather their Pokeballs on his skateboard before kicking it forward with Aitaro. The purple monkey hurls the skateboard into collision with the armoured man, and Crys's Parasect Parapeon, Ruby's Kirlia Ruru, Sapphire's Donphan Phadodo, and Emerald's Dusclops instantly pop up to hold down their foe, causing the man to grunt in frustration.

Crys explains to the Hoenn Dex Holders that it was a conjoint scheme between Prof. Oak, Hoenn's Prof. Birch and the Battle Frontier's owner Scott to dispatch the five of them there, and the scheme has a total of three stages. The initial step was to send Emerald to find and protect the awakening Jirachi as he challenges the Frontier facilities. Then, as the foe appears and the battle is intensified, other Dex Holders are being dispatched, starting with Ruby and Sapphire, who are scheduled to arrive on the morning of the fifth day. Finally, towards the evening, Gold and herself will turn up, and the two of them are the only ones who know of the fact that their petrified seniors have been transported to the Battle Frontier, giving each of them their own missions. Of course, there are always situations out of their original expectations, and Crys puts on a worried look as she steals a glance at the giant sea monster outside.

Guile Hideout giggles that he could understand the unexpected situation they are talking about, which is the fact that they are already too late to do anything, for his wish has already been fulfilled, his wish for a sea monster that would swallow everything, the key to his almighty success. As soon as he says that, his Surskit unleashes a powerful Psybeam, and together with the sturdy repelling force of his sword, knocks back Aitaro, Parapeon, Ruru, Phadodo and Dusclops. The armoured man then commands the sea monster to fill the floor with its giant fins, and the powerful tide of sea water instantly washes the five Dex Holders and their Pokemon towards the other end of the room.

Guile Hideout hops onto the back of the sea monster, and laughs maniacally at the scene. He remarks that it is the first time he has heard of the term Pokedex Holder, being trainers who receive the Pokedex from a scholar of top authority. He directs his attention to Ruby and Sapphire, and recalls how the two thwarted them at Sootopolis. Now knowing that they are such called Pokedex Holders, and many more of their kind are gathering to thwart him once again, he believes it is his perfect chance to wipe them out all altogether, adding further glory to his already acclaimed success.

With that, the man orders the sea monster to wash its fins into the Battle Tower's top floor again, nearly drowning the five trainers, and mocks at their agony with another evil giggle. He then spins around to glare at Jirachi, who is trembling in fear at the man's brutality. Guile roughly yanks at the two long tails of the wish Pokemon, and states that it is of no use to him anymore now that his fish has been fulfilled. With its close to zero inclination towards battling, and the fact that it will return to a 1000-year slumber again in 2 days, he sees no reason why he should keep it, and with a tone of disdain, hurls it violently into the Battle Tower's top floor, where it crashes near the window.

Emerald hurriedly rushes over to help it up, but Guile Hideout orders another strike from the sea monster, who digs its fin into the Tower, aiming straight for Emerald and Jirachi. Fortunately, Latios returns at that moment, and saves the two from peril just in time by blocking the tidal wave with a Luster Purge. Gold then quickly pulls Emerald away from the window and leads everyone to the next room, where they temporarily take shelter behind a wall.

Emerald thanks Latios for its help, and wonders if Anabel and Noland are safe. The mystic dragon replies that the two have joined the other Frontier Brains downstairs, and the seven of them are fighting hard to stop the rampaging rental Pokemon as well as the flood. Sapphire gasps that a flood is taking place, and Ruby rationalizes that the appearance of the sea monster must have caused the island to start sinking.

Outside, Guile Hideout stands on the forehead of the sea monster, and marvels at the scene beneath him. He laughs that he has finally gained possession of the power to rule the entire world, and he will become the ruler of all. After conquering everything with the fascinating power of the sea, perhaps he will also go in search of that mirage Pokemon which is said to be somewhere in the seas.

Back inside the Tower, Sapphire grits her teeth in anger at the armoured man's arrogance, and Crys remarks that it is not the time to take things leisurely now, as they must work to combine their forces to accomplish their goal. Ruby wants to know how exactly they are going to reverse the petrifaction of the seniors and what means they have, and Crys, picking up Jirachi into her arms, states that their only hope lies in wishing upon the wish Pokemon.

Ruby exclaims that they are in big trouble since Guile Hideout has already used the wish for himself, but Gold tells him not to fret, and says what the armoured man doesn't know is that Jirachi has a total of three wish tags, and each time it awakes, it can grant a total of three wishes. Hearing that, Ruby and Sapphire bolt with excitement, and believe that everything can be solved if they use one wish to reverse the petrifaction, and the other to erase their foe. The two clasp their hands with one another in rejoice, thinking that they have a perfect plan going, but Gold and Crys relent that it is not feasible, since there is a pact tied to it.

Ruby and Sapphire wonder what it means, and Crys explains that it is a pact between Prof. Oak and owner Scott. The truth is, when Oak requested to send one of his chosen Dex Holders to the Battle Frontier to protect Jirachi, Scott agreed, but only on one condition, and that is to reserve one quota for himself, since Oak technically required just one wish from the mirage Pokemon. Prof. Oak was startled by the bargain, but Scott argued that he is now lending him his very important Battle Frontier with its many glamorous and groundbreaking venues, which eventually made the old professor concede.

Ruby cannot believe that Prof. Oak would say yes to such a request, and Gold is obviously annoyed by the aspect as well, but says they have no choice but to do as they're told and leave the last wish tag intact. Crys takes another look at the five statues in the room, and sighs that they must work with what they have. She remarks that the top priority is to return Silver and their seniors, Red, Green, Blue and Yellow into their original selves, and Gold nods that it is time that they split their tasks.

With that, Gold orders everyone to send out their flying Pokemon to stall Guile in an aerial fight, and with Crys's Xatu Tupeon taking lead, Gold's Mantine Mantaro along with its Remoraids, Sapphire's Tropius Tororo, and Latios all take flight to begin the midair struggle. Gold then tosses the three metal rings on his billiard cue to Crys, and tells her to take the fashionable lad and wildchild girl with her to explain about the bracelets. Crys beckons to Ruby and Sapphire to follow, and just as Emerald is about to do the same, Gold stops him with the billiard cue, and says there is another task reserved for him, which is to wish upon Jirachi.

Emerald bolts at the statement and wonders why he should be doing it when the wish could be made by anyone, and Gold isn't very happy that Emerald still hasn't figured out why he alone was first sent to the Battle Frontier on 1st July, the exact day of Jirachi's awakening. Comparing the few of them who are meeting Jirachi for the very first time and Emerald, who has fought to protect Jirachi for a few days, it is clear who would find it easier to connect with the Pokemon. Gold turns his back to Emerald and says Oak was the one who decided on this arrangement, and Emerald wonders what Gold's task is. Gold replies that he is assigned as the guardian, and tells the boy to hurry up.

Knowing that he has no other choice, Emerald faces Jirachi, and after a moment of hesitation, utters the wish to reverse the petrifaction of the senior Dex Holders...