At the Battle Frontier, havoc is breaking out in front of the Battle Dome. The Factory rental Pokemon released by Guile Hideout continue to rampage about on the streets, and aimlessly unleash attacks on the screaming press people and visitors who have just left the Dome. The Frontier Brains, Lucy, Greta and Tucker, struggle to hold down the rental Pokemon with Seviper, Umbreon and Salamence, but are obviously being outnumbered and have little success.

Brandon soon comes down from the Dome’s rooftop to join forces with them, and Tucker wants to know where Guile Hideout is. Brandon replies that the armoured man has taken Jirachi with him to the Battle Tower, while Noland has gone off to inform Spenser and Anabel of the situation. The Pyramid King grunts that the four of them are the only ones left to deal with the rental Pokemon now, and encourages everyone to give their best.

Meanwhile, at the Battle Palace, the match for the Spirit Symbol has begun. The Palace Maven Spenser stands silently to watch as his team battles it out with the three Pokemon Emerald left behind. Since trainers are not allowed to give commands in the entire battle, the six Pokemon fight with their instincts, and come up with their own strategies to deal with their opponents. In the first match, Sceptile braces itself against Lapras's powerful ice attacks, and eventually gains the upperhand with its Leaf Blade. Emerald's Dusclops then manages to overwhelm Slaking with its Will-o-wisp and Fire Punch combo, while Sudowoodo engages in a close up struggle with Crobat.

At the accommodation inn, Todd and Latias, who is still disguised as a nurse, are soon made aware of the upheaval outside. They look out from the window, and gasp in shock when they see the chaos in front of the Battle Dome. Latias tells Todd with its telepathy that they must get going as well, and reverts back to its true form. She then grabs the reporter by his shoulders, and without warning, darts out from the windows, causing the young man to let out a little cry of astonishment. Almost immediately, they meet up with Latios outside, and the two mystical dragons share a knowing nod with each other before continuing on their way towards the Battle Palace.

While Latios, Latias and Todd take the aerial route, Noland is running on his feet down below to the direction of the Battle Tower. The Factory Head frowns with frustration as his call via the Pokegear is once again unanswered. A few moments ago, he has managed to inform Spenser about the latest happenings, but for some strange reason, Anabel is not responding to his calls. Uncertain of what could have happened to their leader, and knowing that everything will probably unfold to its fullest by the time evening arrives, the man has decided that the most direct way is to find her at the Battle Tower.

As the Tower's entrance comes into view, Noland catches sight of Emerald and two other young trainers ahead, and calls out to them. Emerald turns around to see that it's the Factory Head, and the boy next to him, who is in red attire, inquires if Noland is also there to chase after the enemy who has captured Jirachi. Noland admits that he is and wishes to know who they are, and the young trainers introduce themselves as Ruby and Sapphire, who have come to assist Emerald in protecting Jirachi. The two place an arm over Emerald's shoulder in a friendly gesture, and grin that they are all trainers who possess the Pokedex and are known as the Pokedex Hoenn Trio.

Emerald instantly yells in protest at their words, and demands to know when have they become a trio. Ruby laughs that if he hates the name Dex Trio, they could perhaps call themselves the Conquer Trio. Emerald frowns in annoyance and fails to understand where the name came from, and Sapphire explains that it is because Ruby has conquered all the Contests in Hoenn; she has conquered all the Gyms; and Emerald will be conquering all the Battle Frontier facilities, making them the Conquer Trio.

Ruby and Sapphire's jolly attitude apparently still irritates Emerald, and the boy hollers that he has no time or interest to mingle with them. Just then, they hear a rumble from the trees behind them, and almost instantly, the Factory rental Pokemon start charging out towards them. Zuzu and Chaka quickly stop their advance with a Mud Shot and Blaze Kick, and Noland grunts that the rental Pokemon which Guile Hideout stole from his facility are now causing a turmoil everywhere on the Frontier island.

Noland notices that Emerald does not seem to have his team members with him, and Emerald reveals that he has left them behind at the Battle Palace for the facility's challenge. The boy takes a look at the painful expressions of the rampaging Pokemon in front of him, and hopes that Noland will agree to let him borrow a few of them to deal with their current emergency. Noland is baffled as to what he is suggesting, and Emerald states that they are just innocent Pokemon exploited by the armoured man, just like his Sceptile was.

Emerald's mentioning of Sceptile being his makes Ruby and Sapphire smile, and the two share a knowing grin with each other while Emerald takes out his E-shooter to aim at the rampaging rental Pokemon. Selecting a Mantine, Mr. Mime, Mawile and Snorlax who seem to be in more severe excruciation compared with the others, Emerald fires off the soil of their respective hometowns, and carves out his signature diamond-shaped markings on the ground. The four Pokemon get enveloped in a burst of warm glow, and are instantly calmed down.

Noland gasps at what he saw, and Emerald hurriedly ushers everyone into the Battle Tower while Chaka and Zuzu keep their attackers at bay. Once the Blaziken and Swampert succeed in backing into the entrance as well, Emerald promptly closes the gates, and manages to shut out the other rampaging Pokemon just in time. The three young trainers pant to catch their breaths, and Noland is amused by Emerald's special ability to calm down rampaging Pokemon in an instant. He grins that Emerald may borrow his rental Pokemon as he wishes, and tells Snorlax, Mantine and Mr. Mime to follow the boy's orders while he takes Mawile himself. He then beckons the young ones to follow him to the elevator, and says it could lead them to the top right away.

In the control room of the Battle Tower, Guile Hideout looks up at the multitude of screens that display the images captured by the surveillance cameras, and grunts that the garbage have arrived earlier than he expected. He points his sword menacingly at Jirachi, and demands to know why it isn't fulfilling his wishes as promised. He spats that it is almost as if the phantom Pokemon could not hear his words, and believes that there must be certain steps to the wishing procedure that he is not aware of. He then decides that it might be a good idea to stall a little bit more time for himself, and motions the silhouette standing behind him to start working.

Down on the ground floor, Noland bangs his fist on the elevator door with a frustrated look, and groans that it is not moving at all. He states that their only other alternative is to scale the Battle Tower floor by floor, and everyone begins heading for the stairs. However, on their arrival to the first floor, the overhead lights on the ceiling suddenly come on, and Emerald wonders what is going on. Noland explains that it is the facility's lighting system used during challenges, but fails to understand why they are being activated.

In that instant, a Ninja Boy materializes in front of them, and sends out a Gulpin to attack. Emerald gasps that it is a virtual trainer, and the group soon spots a familiar silhouette standing on the other end of the room, who is no other than Anabel herself, the Frontier Brain in charge of the Battle Tower.

Yet, something seems wrong with the Salon Maiden. Unlike her usual charismatic self, the sparkle of confidence is missing from her eyes, and she stands with a blank look on her face as if she is just a puppet under someone else's control...