On the first floor of the Battle Tower, Noland and Emerald gasp in surprise as the silhouette standing on the other end of the room reveals itself to be Anabel. However, something seems wrong with the Salon Maiden. The sparkle of confidence in her eyes is strangely missing, and she wears a blank look on her face as if she is merely a puppet under the control of someone else. Noland and Emerald call out in unison to the Frontier Brain leader, but the girl gives no response, and simply turns around to leave without a word.

Noland jumps to his feet and begins to give chase, but the virtual Ninja Boy in the room refuses to let him pass and calls forward his Gulpin to attack. Fortunately, Mawile cuts in to stop its lunge, and narrowly saves the man from the powerful impact. Noland puts on a worried look as he remarks that something is clearly wrong with Anabel, and says she doesn't seem to be her usual self at all.

Sapphire suggests dealing with the virtual trainer first, and believes that they will be able to find out more on the upper floors. Noland agrees and orders Mawile to slam down the Gulpin, which manages to knock out the poison Pokemon in one hit. The group then rushes upstairs, but to their surprise, another virtual trainer, this time a Kindler, takes form and sends out a Numel. The group makes an effort to defeat the fire camel, and proceeds to the next floor. Unfortunately, they once again find themselves face to face with a virtual trainer, a Bird Keeper this time, who commands a Taillow.

In that instant, Noland realizes with a start that they are no different from doing an actual challenge of the Battle Tower. Being the tallest and toughest facility in the entire Battle Frontier, the Battle Tower requires challengers to defeat the virtual trainer on each floor as they ascend the building, and only those who manage to survive will be able to engage in a final combat with the Frontier Brain Anabel, who waits on the very top floor.

The thing is, only Anabel herself and their owner Scott possess the means to activate the facility's virtual trainer system, and right now, the system has clearly been switched on to thwart their advance, with evidence pointing to Anabel being the one responsible for it. Noland's mind boggles at the possibility that their leader has sided with Guile Hideout, but on a deeper thought, rationalizes that it will be more logical to suspect that the girl is under the control of the enemy.

At that moment, Guile appears on the monitor screen in the room, and laughs maniacally that Noland's postulation is indeed correct. He snickers that he has successfully taken over the entire system of the Battle Tower, and the group will not be able to reach him until they have completed the Tower challenge in accordance to the rules, which call for 10 sets of knock-out battles each consisting of 7 individual virtual trainers.

Noland clutches his fist in anger, and demands to know what the armoured man has done to Anabel, or more precisely, how he managed to go near her. Guile lets out a giggle, and suggests the Factory Head recall carefully his last encounter with the Salon Maiden. Noland thinks back on an earlier time when they were watching the match between Emerald and Tucker at the Battle Dome, and remembers how Anabel excused herself from the group to leave with Scott on his flying saucer for a private meeting. Realization suddenly hits like a radical in his mind, and the man hastily makes a call on his Pokegear to contact their owner.

Scott soon answers with a gasping voice, sounding as if he is out of breath, and finds it odd that Noland is asking of his whereabouts during Emerald's Dome challenge. He replies that he was staying among the press people at the spectator stand, and gets even more baffled when Noland inquires about his private meeting with Anabel, since he has actually not met her the entire day. Right now, he is being chased after by the Factory rental Pokemon which Guile Hideout sent rampaging everywhere, and the chubby little man steers his flying saucer sideways as he narrowly evades another combined attack from a Xatu, Dustox and Shuppet.

A horrified look breaks out on Noland's face as he realizes that the Scott who has been accompanying them at the Dome's Frontier Brain private stand was actually not the real one. Guile laughs that whom they saw was just an illusion created by the powers of psychic Pokemon, and Noland furiously calls him a despicable person. However, Guile simply takes it as a compliment, and smirks that while he normally lacks minions to work for him, he now has the entire Battle Tower's unlimited amount of virtual trainers and rental Pokemon to serve as his slaves.

Somehow, Guile's use of the word 'slave' hits Emerald like a cold dart, and the boy abruptly breaks into a fury, hollering that he will not forgive the armoured man for what he did. Guile giggles that he should save his heroic statements until they meet on the top floor, and wishes him good luck in the streak of 70 consecutive wins which he must first obtain in order to reach there. With that, the monitor screen goes blank, and the group is once again left alone in the room.

Emerald wastes no time, and rushes up the next flight of stairs with Mantine, Mr. Mime and Snorlax. The others quickly tag along, and Noland grunts that it seems like their only choice is to play by the rules and conquer the tower floor by floor. He states that they should work together however, and leave only one person to deal with the virtual trainer each time while the others keep advancing. In that way, they can proceed much quicker, and will hopefully speed up their pace by at least 4 times. Ruby and Sapphire nod in agreement, and the four trainers promptly begin their group challenge at the Battle Tower.

As the group advances with the strategy of one after another from floor to floor, Noland gradually notices from his momentary observations that just like Emerald, Ruby and Sapphire both demonstrate highly trained battle skills that one would never expect from someone at their age. He muses that it must be the unique strength of the Pokedex Holders, and knows that he must give his best to keep up as well if he is ever to rescue Anabel from the enemy's evil clutches.

Unleashing their full power on the opponents, the group soon makes it to the last few floors of the building, and are about to reach the Battle Tower's summit. On the 67th floor, Chaka delivers a Blaze Kick and faints an Ivysaur with one hit. On the 68th floor, Zuzu unleashes a Mud Shot from its mouth, and blasts a Heracross across the room. On the 69th floor, Mawile swings the jaw-like horn on its head, and rams it hard into a Trapinch.

Ruby eventually defeats the virtual trainer he is facing, and advances to the 70th floor, the top floor, where he meets up with Sapphire who has just arrived as well. Sapphire wonders where Emerald and Noland are, but Ruby says he has no idea, since he directly headed for the stairs once he saw that someone is already dealing with the floor's virtual trainer, and didn't really pay attention to who was engaging in the battle.

The two young trainers proceed into the room ahead, and discover that it seems to be some kind of display hall instead of the usual arena setup on the other floors. Maps of various regions hang on the walls, which are lined by closely packed bookshelves that have an assortment of old and new books sitting on them, as well as giant glass cabinets that contain ship models and ancient scripture within. Ruby realizes that the place is actually a data room, and marvels at the diverse and large amount of materials that have been collected from across the land.

They soon spot a poster on the far wall, which is a memoir of the Battle Frontier's construction from beginning to completion, written by the owner Scott himself. Unable to decipher formal characters, Sapphire has trouble understanding the lines, and Ruby decides to read it out loud. Apparently, while Scott's primary intention behind creating the Battle Frontier is to put together a collection of facilities that provide the foremost style of Pokemon battling to trainers all over the world, he has always known that the soul of the place lies in the people but not the buildings. Therefore, he has put extra effort and taken a considerable amount of time in finding suitable trainers, long before the construction even began, so as to give each facility a most fitting Frontier Brain.

Ruby remembers hearing all about it from his father Norman, that Scott has journeyed far and across regions to seek out powerful trainers, and recalls how the Petalburg Gymleader himself has been asked to keep an eye out for the man. Looking up at the cheerful group photo of Scott and the Frontier Brains, which was taken during the inauguration of the Frontier's construction, Ruby and Sapphire see that the seven individuals are whom Scott eventually selected, and can't even bring themselves to imagine how many skilled trainers the Frontier owner must have screened before making his final choice.

The two young trainers continue to wander about in the data room, and Sapphire suddenly lets out a cry of disbelief as a small platform with 5 statues on top comes into view. She exclaims that it is a corner dedicated to the Pokedex Holders of each generation, and rushes over excitedly. Ruby muses that it would make the featured trainers their senior in that case, and Sapphire begins to flip through an album on a stand which has detailed information on the Kanto and Johto Dex Holders, wondering when Ruby and herself will earn the privilege to have their names included. Ruby is amazed that even statues have been specially made for the corner, and sees that the ones being depicted are the four Kanto Dex Holders, Red, Green, Blue, Yellow, and a Johto Dex Holder, Silver.

Just then, a loud crash rumbles across the entire floor, and Ruby and Sapphire realize that something is going on in the adjacent room. The two hurriedly bolt towards the connecting door, and gasp in shock when they see that Emerald has actually been engaging in a battle with Anabel all this time. Clearly, Emerald was the first among their group to reach the top floor, and has already challenged the Salon Maiden to the final match. However, from the look of things, Anabel's Raikou is gaining an overwhelming upperhand, as Emerald kneels to catch his breath while his Mantine, Mr. Mime and Snorlax lay sprawled across the ground.

The thunder beast charges forward to deliver another swipe, and sends Emerald and his team flying, breaking one of the boy's magic hand extensors during the process. Sapphire cries that the three Pokemon won't be able to last much longer, and urges Ruby to give help. However, Emerald demands the two of them to stay where they are, and says he is having an official combat with Anabel, which must not be interfered. Raikou continues its assaults, and swings its powerful right paw upwards, hurling its opponents across the room and knocking the boy's platform shoes off at the same time.

Sapphire finds it hard to believe that Anabel is such a cruel person, but Ruby reminds her of the distant look in the Salon Maiden's eyes, and states that the truly cruel one is Guile Hideout who is controlling her from behind. Sapphire grits her teeth in anger, furious that someone can be as merciless as the armoured man is, and wonders who his real identity could be. Ruby takes out his Memory Fire Lighter to replay the recordings in front of the Battle Palace earlier, and Sapphire questions if he is still suspecting the Palace Maven Spenser.

Ruby states that the old man has referred to Sapphire as a compatriot after making reference to her past contact with the Blue Orb, suggesting he himself has done the same thing. But Sapphire remarks that the fact alone doesn't make Spenser a bad person, and Ruby admits that he has trouble linking up the two things as well.

Emerald once again gets swept off his feet, and crashes hard onto the ground. His body starts to ache from all his injuries, and his determination begins to falter as Raikou towers over him with a menacing look. In that instant, he hears his name being called via telepathy, and is demanded to stand back up since he still hasn't lost yet.

Emerald looks up at the open window of the room to see Latios hovering outside, and the mystic dragon says it has something to deliver. With that, it releases its clutch on the three Pokeballs it is holding, and Emerald gasps in surprise upon seeing his Sceptile, Sudowoodo and Dusclops inside. The three Pokemon grin and wave at their trainer with victorious gestures, and Emerald wonders if it could be what he is thinking. Latios tosses a golden badge which has the letter S engraved on it, and says his trusted three have conquered the Palace challenge and earned the Spirit Symbol for him. The eon Pokemon adds that the three are still buzzing with determination to fight, and Emerald puts on a contented grin before releasing them out from their Pokeballs.

The boy declares to Anabel that their match shall go on, but the Salon Maiden suddenly trembles and collapses onto the ground, much to everyone's surprise. A clanking sound instantly fills the room, and Guile Hideout soon appears with his sword in hand. The armoured man steps his foot on Anabel who has now lost consciousness, and grunts that he has clearly overestimated the girl's ability to withstand the stress of his mind control.

Emerald shoots a look of anger and disgust at the man, and Ruby wonders if the body under the armour could really be Spenser. However, Latios speaks via its telepathy again upon hearing Ruby's query, and sighs that they seem to be placing a faulty suspicion on someone who is completely innocent. It states that it should perhaps show them a moment of truth, and says it will now project to them what Latias is currently seeing at the Battle Palace with their unique ability to share visions with each other.

In a flash of light, Ruby, Sapphire and Emerald find themselves in Spenser's underground chamber at the Battle Palace, where the Palace Maven is standing in front of a giant mirror, with his back facing the reporter Todd and Latias. Spenser states that what he is about to tell them is part of a painful memory which he never wishes to talk about again, but knows that he has no other choice in light of the current crisis they are facing.

Many years ago, Spenser paid a visit to his two close friends at Mt. Pyre, where the legendary Red and Blue Orbs were guarded in a small cave on top. Although his friends have warned him not to go near the mystic jewels, he eventually succumbed to temptation under the stunning beauty of the Blue Orb, and reached out to stroke it when he was left alone in the cave. In that split second of contact, he felt an extraordinary surge of energy rushing through his fingers, through his wrists and arms and finally reached his shoulders. Out of fear, Spenser withdrew his hands immediately, but it was already too late.

From that night onwards, Spenser felt progressively unsettled in his heart and mind. He started to get recurrent dreams of a giant sea monster which he failed to shake off, and his eyes slowly became dull over time. Todd wonders what kind of sea monster it was, and Spenser states that although he was unsure at the beginning, he later learnt that it was one of Hoenn's legendary Pokemon, Kyogre.

The revelation causes everyone to gasp in surprise, all but Guile Hideout who keeps a cold expression. Spenser remarks that he deeply regretted about what he did, but knew that there was no one to blame but himself. He felt terribly ashamed of his weak mind, and thus began forcing himself into strengthening his heart and spirit. It was therefore no coincidence that he is now earned his name as the Frontier Brain of the spirit.

Spenser points out that even though he has already managed to grow out from his nightmares, certain scars are permanent, which allow him to recognize those who have stepped into the same darkness as he had. He explains that the dull light developed within one's eyes upon contact with the Blue Orb will never go away, and it was the reason why he knew of Sapphire's past history with the jewel by simply looking into her eyes. The thing is, there is someone else whose eyes he saw such a distinctive glow in, and while he was simply suspecting during their first encounter at the Artisans Cave, he is now certain that the person indeed shows the same dull light in his eyes.

Todd bolts with surprise at what Spenser is suggesting, and the Palace Maven turns around to come face to face with Guile Hideout via Latios and Latias's telepathic vision, stating that the armoured man is the other someone who has come into contact with the Blue Orb, and is now clearly obsessed with the tremendous powers which the mystic jewel offers.

Guile laughs that Spenser truly lives up to his name as a Frontier Brain, and reveals that the Blue Orb has in fact inhabited his body in the past, which gave him a chance to experience the unmatched exhilaration of being as one with the jewel's unlimited power, something he will remember for the rest of his life. He then giggles that he shall unveil himself since everyone is so interested to know his identity, and proceeds to lift up the metal mask on his helmet.

To the horror of Ruby and Sapphire, a familiar face gradually comes into view, a face which they will never forget, the face of the evil leader of Team Aqua, Archie...