On the top floor of the Battle Tower, Guile Hideout giggles that he shall unveil himself since everyone seems so desperate to see, and uncovers the helmet mask he is wearing, causing Ruby and Sapphire to cry out in disbelief. It turns out that the armoured man they are facing all this time is actually an old foe whom they have already faced before, the same person who brought crisis to the region of Hoenn less than one year ago, the evil leader of Team Aqua, Archie.

Sapphire fails to understand how the man managed to survive their deadly fight at Sootopolis, and cannot believe that he has returned once again. Archie grins that they must think of him as a very stubborn person, and admits that he indeed is, for he is still clinging onto his grand dreams to expand the sea. The truth is, when he got possessed by Kyogre and was spiritually linked with the ancient titan, he finally experienced in person how endless the powers of the ocean could be. By becoming one with the sea once more, he will be able to claim the infinite power it holds, and rule the entire world with it.

Ruby calls Archie a crazy maniac, and Sapphire demands to know if he plans to awaken Kyogre a second time. The armoured man giggles that it wouldn't be necessary, and points his finger to Jirachi, stating that the wish Pokemon alone will be sufficient to fulfill his dreams. At that moment, Mawile charges towards him from behind, but the man timely calls out his Tentacruel and blocks off its ambush.

Ruby, Sapphire and Emerald turn around to see that Noland has arrived, and Archie remarks that he has been waiting for him. Without warning, Tentacruel wraps its tentacles around Anabel, who remains unconscious, and hoists her up in mid-air while Archie places the blade of his sword on her neck. Everyone bolts in horror, and Noland demands the armoured man to let her go. However, Archie puts on a smirk, and says he will have to exchange the favour by telling him the interpretation of the Jirachi report's last page, something which as the Frontier Brain of knowledge, he must have successfully deciphered.

The dilemma has clearly stumped the Factory Head, and he trembles with hesitation as he has trouble deciding what to do. On one hand, disclosure of the crucial information on Jirachi's report to the enemy will lead to disaster, but there is no way he can sacrifice a companion who has shared and gone through so much with him.

Seeing the distress on Noland's face, Archie snickers with disdain, and motions to Tentacruel. Instantly, the poison jellyfish lashes out a tentacle to strike at Noland, and snatches the Jirachi report from his pocket before hurling him across the room together with Anabel. Archie quickly flips to the last page, and reads that in order to make a wish on Jirachi, one must look directly at the third eye on its abdomen. The armoured man finally understands why the phantom Pokemon did not respond to his words earlier, and grins that this third eye seems to be where the point what is referred to as its center of life force is.

Archie nods at his Surskit, and the water bug swiftly targets a Psybeam on Jirachi's belly. The wishing star spasms with agony, and struggles to keep its true eye shut. Unfortunately, it eventually loses the fight, and a turquoise coloured eye blinds the room with a shimmering flash as it snaps open in the center of its abdomen. Archie grabs the moment to fix his gaze on the third eye while making his wish, and a blank look soon washes over Jirachi's face as the green tag on the right side of its head begins to wiggle. Ruby, Sapphire and Emerald gasp in shock when they see letters slowly appear as Star Symbols on the tag, which writes 'To rule everything with the power of the sea', and bolt with realization that the armoured man's wish must have successfully channeled through to Jirachi, and is about to manifest.

In that instant, stormy waves start to form in the open seas surrounding the Battle Frontier island, and a gigantic whirlpool blasts out from the oceans with a tremendous force up into the air, gradually taking the shape of an enormous killer whale resembling the appearance of the ancient sea titan, Kyogre.

Lucy, Brandon, Greta and Tucker, who are still fighting the Factory rental Pokemon, look up from where they are, and exclaim with astonishment at the giant creature that is looming over the entire Battle Frontier. Back in the Battle Tower, Ruby at first thinks that Kyogre has been awakened again, but on a closer look, realizes that it seems to be even bigger in size. Sapphire notices that the creature merely has the outline of Kyogre, which content is still nothing but seawater, and gasps that it is essentially a creature born out of the sea itself.

Archie laughs that it is exactly what he wanted, and reveals that he has wished for a sea monster that is capable of swallowing up everything. Ruby is bewildered that Jirachi has made such a wish possible, and Sapphire fears that this creature will be even deadlier than the actual Kyogre.

Noland falls to his knees next to Anabel with a defeated look, and grunts that although he has managed to save a companion, this dream place which they have built together will now disappear into the bottom of the ocean, the worst scenario anyone of them could have ever imagined. Archie giggles that from his standpoint, it is the best scenario he could ever imagine, and begins to laugh even harder. Sapphire tells Noland that it is not a time for despair, and says he has already rescued Anabel, and what they must do now is to think of a way to turn the situation around.

At that moment, Archie suddenly winces with discomfort, and remarks that he has forgotten not to show his face for too long. He quickly tugs down his helmet mask, and his action catches Ruby's attention. The boy finds it odd that Archie still needs to cover up himself even though his identity has already been revealed, and starts to wonder if the armour was not meant for disguise purposes after all.

Once again taking the appearance of Guile Hideout, Archie bids everyone farewell, and hopes they will enjoy living among the seaweeds. With that, he turns around to leave and heads back into the Frontier data room next doors. At the same time, the looming sea monster lunges forward, and washes across the entire Battle Frontier like a giant tsunami.

Powerful waves flood into the Battle Tower's top floor through its open windows, and everyone struggles to brace themselves against the strong current. Once the first wave has passed, Emerald tells Latios to take Noland and Anabel to a safe place, and the mystic dragon quickly pick up the two Frontier Brains to jet off. Ruby sees that the sea monster is turning around, and attempting another dive, and hollers that they must get themselves out as soon as possible as well.

Just then, the three hear a clank from the direction of the windows, and look over to see the Guile Hideout climbing in. However, something seems weird with the armoured man. Not only is his height shorter and built leaner than he used to be but his gestures and movements are oddly comical as he wiggles his arms and legs around to shake himself dry. He then coughs uncomfortably and asks if everyone is all right, and beckons them to follow him.

Ruby, Sapphire and Emerald remain motionless at Guile's eccentric behaviour, and suddenly see the saw-tooth shaped gates leading to the data room closing vertically. The armoured man exclaims that the sea monster's impact earlier must have activated the Battle Tower's auto-defence system against disasters, and urges everyone to hurry while he runs over to pull on Sapphire's arm. His unexpected action causes Sapphire to bolt with astonishment, and the girl promptly delivers a kick on his back to send him flying through the closing gates and into the data room.

Ruby remarks that the armoured man has a point despite his sudden display of weird manners, and says they won't be able to escape once the gates are shut. The three young trainers thus dart towards the opening which is closing in from above and below, and throw themselves through it. Unfortunately, while Ruby and Sapphire manage to make it, Emerald gets caught between the saw-tooth gates, and Sapphire cries that his saggy clothes are holding him back.

Emerald cringes in agony as the pointed gates start to clamp down on him, and Ruby and Sapphire try with all their might to free him but to no avail. Suddenly, a black rod is hurled between the closing gates, and temporarily halts their advance towards each other. Ruby quickly flips out a pair of scissors from his stitching kit to cut open the back of Emerald's clothes which is caught by the saw-tooth edge, and Sapphire carefully drags him out until his whole body goes through.

Thankful for the black rod which saved them, Ruby, Sapphire and Emerald turn around to see who their rescuer is, and bolt with shock and disbelief when they discover that it is no other than Guile Hideout. The three leap back with apprehension as the armoured man walks over to the gates to retrieve the rod, and think they must be dreaming when the man grins that they had a really close moment.

In that instant, a voice booms with fury in the room, and the three young trainers gasp in surprise when they see another Guile Hideout walking towards them with his sword in hand, demanding to know who his impersonator is. Emerald sees how this second armoured man looks more like the one they used to know, and realizes that he is the real Guile Hideout while the one who helped them is just an imitator.

The fake armoured man holds up the black rod which he used to stop the gates, and extends it out to form a billiard cue. He then relents that he has been busted after all, and says he has initially planned to disguise as Guile Hideout and trick his way through Surskit and Tentacruel until he gets to Jirachi. Clearly, his plan has failed and thinking back now, it was a really stupid strategy to start with.

The real Guile Hideout loses patience from hearing all the babbling, and demands his impersonator to shed his fake exterior. With that, he swings his sword forward for a slash, and instantly splits the other armoured man's metal outfit into half. The impersonator grins that Guile Hideout shouldn't be the one passing accusations on identity faking, since he has fooled Anabel with a fake Scott himself, but adds that tricks really don't matter in battles as long as one is careful enough.

As Ruby, Sapphire and Emerald watch in astonishment, the heavy armour falls apart with a loud clank to reveal a teenage boy who is wearing shorts and a red sweater. The boy calmly pulls on a cap over his jagging hair to face it backwards while fastening a pair of goggles on top, then flips out a bag of Lava Cookies to munch on, stating that it would be a waste not to try out Lavaridge's famous snack on one's first visit to Hoenn.

With a nonchalant expression, the boy announces that there is change of plans, and tells his companion to show herself. A girl who has two ponytails arching upwards instantly storms out from her hiding place with an annoyed look, and says she knew he would be making such impulsive decisions without informing her in advance, which is why she strongly objected to this strategy right from the beginning, so as to save the big sum of money involved in making the armour. With that, she stuffs a bagpack back to the boy, causing him to call her the chairlady of Club Serious like he always does.

Emerald gasps in surprise that Crystal, the one who has provided him with Pokemon for facility challenges so far, has also come to the Battle Frontier, and the girl grins that she and Gold, her fellow Johto companion, are there to give support. Gold looks over to Ruby and Sapphire, and says they must be the fashionable lad and wildchild girl. He then pats Emerald on the head, calling him the unorthodox boy, and says his funky croissant hairdo will surely surprise Explotaro.

Ruby and Sapphire recall seeing the two's faces in the data room's Pokedex Holder profile book earlier, and exclaim that their seniors have arrived to help. Sapphire immediately becomes frantic upon the realization, and rushes up to Crys to shake her hands vigorously. She thanks them for being there, and wonders if the other five seniors will be coming as well, but a solemn look instantly shows on Crys's face, and the girl shifts her gaze downwards without a word.

Gold remarks that the other five people won't be coming to help unfortunately, but in a sense, they have already arrived. His statement causes Ruby, Sapphire and Emerald to frown in confusion, and Sapphire requests to know what it means. Gold sighs that it is a long story, but to put it short, instead of the other seniors coming to provide help, they are there to help the five of them.

Guile Hideout grunts in frustration, and says he has heard enough of their pointless talk. He hollers that he has no idea what a Pokedex Holder is, but no one will be able to get in his way or stop him right now. He swings up his sword and begins to charge forward, and Gold swiftly tosses out his billiard cue and two Pokeballs to call out Explotaro and Aitaro.

The Typhlosion and Aipom immediately take on fighting stances upon popping out, and the little monkey catches Gold's billiard cue with its palm-like tail. It then twirls it around rapidly as Explotaro powers up the flames on its back, and the combined actions create a tornado of fire that explodes towards the armoured man. Guile Hideout holds up his sword to fend off the attack, but quickly finds himself losing ground, and ends up being blasted across the room.

Sprawled on the floor next to his Surskit, Guile gasps in astonishment at the power of the flames, and Gold hopes that the sly bastard has learnt his lesson, and will never show his face again. The boy turns around to steal a glance at the five statues standing in the Dex Holders' corner of the room, and thinks to himself that out of the three wishing tags of Jirachi, only two more can be wished upon. He reaches into his pocket as he walks over to Silver's statue, and places a metal ring on his hand, promising his good ol' pal that he will regain freedom very soon.

Gold takes out three more similar metal rings to hang on his billiard cue, and digs into his bagpack to pull out his skateboard. Hoisting his billiard cue over his shoulders, he puts on a confident grin, and announces that it is time to begin the ceremony. Behind him, Ruby, Sapphire, Emerald and Crys stand next to Zuzu, Chaka, Sceptile and Megapeon, and get ready for their final battle. On the opposite side of the room, Archie holds an anxious gaze on the young trainers under his armour, and a cold sweat slowly trickles down his forehead...