At the Hoenn Branch Pokemon Storage and Transfer Management Center, Lanette sits in the office she shares with her elder sister, Bridgette, and wonders why the person on the other side of the line is not speaking. The sisters' two Swablus chirp merrily as they fly around in the room, and Lanette keeps talking through the receiver but gets no response.

She soon manages to hear some muffled murmurs, and begins to freak that they are receiving mysterious calls. But Bridgette, who barely shifts her gaze from the computer, calmly points out that the speaker phone mode has been switched on, and Lanette realizes that she has accidentally done so when she knocked down her pile of books earlier.

Setting aside the receiver, she fumbles through the mess on her table, and soon finds the body of the telephone. She apologizes to the caller for taking so long to answer, and is quickly greeted by Bill and Celio, their long time colleagues living in Kanto. Bill hopes that everything is well with the sisters, and reveals that he and Celio are currently at the Sevii Islands, and are faced with some big trouble. He states that to solve the crisis, he will need to borrow the knowledge and talent of Bridgette and Lanette, and hopes the genius sisters, who are in fact the co-inventors of the Pokemon Storage and Transfer System, will be able to help them out.

Meanwhile, at the Trainer Tower on Seven Island, Mewtwo struggles to free itself from the white armour but to no avail. It feels as if all its powers are restrained by the device, and Red hurriedly orders Saur to break it with a vinewhip. However, the attack barely scratches the armour, and Giovanni grins that the M2 Bind, specially designed to restrain Mewtwo, is linked to system of the Trainer Tower's mother computer, 'r'. Snapping his fingers, he orders 'r' to elaborate, and to everyone's surprise, virtual eyes start appearing on every single crystal liquid sphere along sides of the corridor, and the machine soon resumes its signature eerie chuckle.

Green gasps in shock that Porygon2's zapcannon earlier didn't manage to destroy 'r', and the computer laughs that it was simply shut down temporarily. It then chuckles that the M2 Bind works in a similar fashion to the restraint devices which held Oak and Blue's parents, but is one zillion times stronger, and has the ability to disable a Pokémon's attacks as well as slowly drain its strength.

Just then, 'r' detects movement in its network system again, and brags that the same tactic won't work twice. Before Porygon2 manages to move any further, a virtual lock clamps around its neck, and traps it within the virtual space. Green grits his teeth in frustration, and 'r' begins to laugh maniacally. Giovanni sweatdrops that although 'r' is a very sophisticated computer system, it was developed by Jagura who must have programmed his style and manners into it as well. Nevertheless, the TR leader believes that the battle is now over, and Red demands to know why he makes such a claim.

Putting on an evil smirk, Giovanni points out that Deoxys has already activated all of its forms, and one of his scheme's biggest threats, Mewtwo, has also been restrained by the M2 Bind. The only ones who could oppose him now are the Pallet trainers, Red, Green and Blue. However, the Deoxys-Divides will keep them occupied at the Trainer Tower, enabling him to focus on finding his lost son without worries. The man then lifts himself off on Crobat, and bids the young trainers farewell.

But Green is not ready to let the TR leader go. He leaps up to grab him by the jacket, and says he finds it hard to believe that the previous Viridian gymleader, being his predecessor, is such a wicked person. He hollers that when he found the book 'The Mysteries of The Earth' which Giovanni left behind in the gym, he thought the man would at least be a dignified person, but he now starts to question whether he has been wrong all along.

Giovanni, on the other hand, does not see what a big deal it is, and coldly states that what the boy thinks has nothing to do with him. He ruthlessly tosses Green down, and sends him crashing into the wall before taking off on Crobat through the central opening at the roof top of the building.

As the gang of Deoxys-Divides close in on Red, Green and Blue, the three young trainers wonder what they should do and think hard to come up with a plan. Suddenly, a hyperbeam blasts through the wall from outside, and sweeps the creatures across the room. The three look over to see Brinca, Lorelei and the Sea Gallop sailor on Dragonite, and the old lady grins that the beautiful backup forces have arrived.

Red and Blue are thankful that Brinca has come, and Brinca is also glad that they have successfully rescued Prof. Oak and Blue's parents. She offers to take the three of them to a safer place on her Dragonite, and Blue's parents turn around to give their daughter a longing look. Blue fully understands what her parents are thinking, but also knows what she must do. She assures them that they are the most important thing to her in the world, and wishes that their reunion have not been interrupted by all this. However, she also carries the destiny to fight the evil, a responsibility she has taken upon her shoulders since she separated from them. She apologizes that she must stay behind to do her duty, but promises her parents that she will come back, come back very soon with a smiling face when all evil has been taken care of.

Accepting their daughter's decision, Blue's parents fight back their tears and give her a nod of encouragement before climbing onto Dragonite. Brinca states that she shall remain to join the fight, and wonders if Lorelei will command Dragonite and bring them to safety. Lorelei grins that she has no problem with that, and hears Blue calling out to her. The young girl hopes the ice queen will take good care of her parents, and Lorelei assures her that she will do her best.

Green then notices that the Deoxys-Divides are starting to recover from their injuries, and urges Oak to leave with Blue's parents quickly. But the professor announces that he shall stay behind as well, and says he still has unfinished business in the Trainer Tower. Grabbing Blue by the wrist, he wants the girl to come along, and dashes for the stairs. Several of the Deoxys-Divides begin to give chase, and Blue wonders where they are going. Oak states that their three Pokedexes are still in the building, and they must go retrieve them immediately.

Back at Bridgette and Lanette's office, the sisters are astonished to hear Bill's story of how Deoxys morphed into a new form after being exposed to the powers of two mysterious stone plates, known as Ruby and Sapphire, which, according to the Team Rocket secret agent Storc, carry the unique climate of Hoenn, the region where Bridgette and Lanette are currently residing.

Lanette makes sure that she didn't hear it wrong when Bill said the creature morphed but not evolved under the effect of the stone plates, and wonders what her sister thinks. Bridgette remarks that she has no idea and is simply guessing, but proposes if it might be similar to how certain Pokémon species can show different physical appearance with no evolution involved. For instance, every Spinda has different patterns on their bodies, and there are a total of 28 different forms of Unowns discovered.

Celio, however, doesn't seem too convinced by the theory, and points out that although those species have varying physical appearance, they will not morph into one another. Bridgette thinks again, and suggests if it could be like how Castform changes its form under different weather effects. Lanette promptly echoes the thought, and believes that they are on the right track. Castform is a Pokémon which changes forms according to weather. Replacing the term 'weather' by 'climate', it would pretty much sum up what Deoxys is, a Pokémon which changes forms according to climate, which takes into account its environment and geographic location.

Bill exclaims that it must be the case, and recalls that two of Deoxys's forms, attack and defense, have been around since the very beginning, which are most likely influenced by Kanto's climate. Its speed and normal forms, which were not fully activated until its exposure to the Ruby and Sapphire plates, are logically unique to Hoenn's climate, and the two mysterious stones must have somehow recreated the Hoenn climate in Kanto, enabling these two forms to manifest.

The young man praises Bridgette and Lanette for truly being the genius sisters, and feels grateful that he has contacted them. Bridgette remarks that it is too early to be happy, and says there are still things that they have to find out, in particular the source of the two mysterious stone plates. Bill decides to entrust Celio with the investigations, and thanks the sisters again for helping out. Bill then rushes out and thinks to himself that if this new speculation of theirs proves to be correct, they will be able to put an end to all this very soon.

At the meantime, at Viridian City, a young girl in cowboy outfit, who has her yellow hair tied up into a long ponytail, is trying hard to keep up with her Pikachu running ahead. The female Pikachu, named Chuchu, stops in front of the Viridian Gym, and the girl pants to catch her breath, remarking that she is feeling a bit nervous having not seen them for such a long time. She wonders if Green has already returned to the gym, and grins that Chuchu must be very excited since Red is most likely together with Green, which means Pika will be there as well.

The girl yells out her greetings as she pushes open the gym's front door, but sees that there is actually no one inside. She wanders into the empty room, and is surprised that Green is still not back yet. About a week ago, she heard that Green went back to Pallet with Red after receiving Prof. Oak's summon, and figured that he should be back by now. However, from the looks of things, it seems that whatever business the professor wanted from them is going to take a little longer.

Suddenly, the girl feels a presence behind her, and lets out a squeal when she turns around to see Green. The boy welcomes his challenger before introducing himself as the Viridian gymleader, and apologizes for his absence due to urgent business. The girl realizes that it is just a virtual image of Green, and the boy goes on to say gym challenges are still possible because he has left his team behind. A platform then opens up on the ground of the gym, and Green's Pidgeot, Alakazam, Arcanine, Exceggcutor and Ninetales appear through the opening.

The virtual image of Green states that beating his Pokémon without his presence would still qualify the challenger the Earth Badge, and the girl suddenly feels Chuchu tugging at her clothes. She kneels down to read the Pokémon's mind by placing her palm over it, and discovers that it wishes to fight. After thinking for a brief moment, she decides that it would be fun to do a gym challenge, and the virtual Green proceeds to commence the battle.

Green's Pidgeot swiftly flies to the center of the stage to unleash a featherdance, and Chuchu barely manages to dodge when the big bird strikes down with a wing attack. Pidgeot then hovers back, and Alakazam takes over as the active Pokémon on Green's side. It starts off by flashing its spoons at Chuchu, and the girl gasps that it has used roleplay to copy her Pokémon's static ability. Alakazam follows up with a powerful thunderpunch, and knocks Chuchu across the room, fainting it and paralyzing it at the same time.

The girl rushes over to pick up her Pokémon, and laughs embarrassedly that they have lost. She apologizes to Chuchu for giving it such bad commands during the battle, and muses that Prof. Oak was indeed right when he named Green the Raiser, as his Pokémon have been raised so well that they are able to fight on their own even without their trainer's directions.

Just then, the girl notices that the half broken statue of the previous Viridian gymleader is still standing at one corner of the gym, and thinks to herself just how much more responsible Green is compared with this man. When this previous Viridian gymleader disappeared many years ago, the Viridian Gym was left completely abandoned. No one tended to it until the selection test held by the Pokemon Association several years later, in which Red earned the gymleader qualification, but ended up giving the post to Green instead.

A lot more has happened since then, but the girl realizes that she has been reminiscing about the past too much, and decides to heal Chuchu's wounds. She hugs the electric Pokémon tight to her chest as a warm glow emanates from its body, and all of its injuries are gone within seconds. The girl comforts Chuchu that it shouldn't feel too bad since it was Green's Pokémon that they fought against afterall, and Chuchu looks up at its trainer with a grin.

The two then exit the gym, and the girl wonders what kind of new quest Prof. Oak has sent Red and Green on. Suddenly, she spots someone from a distance, and thinks that it must be another gym challenger. However, as the person gets closer, she realizes that it is someone she has seen before.

With the Viridian Gym coming into sight, a red haired boy tells his six Pokémon that they have finally arrived at Viridian. Shifting his gaze to the road ahead, a familiar face catches his attention, and he knows right away that he has seen that girl with a ponytail and the Pikachu next to her before.

After a quick moment of thought, remembers her as one of the Kanto Pokedex holders named Yellow, who uses a female Pikachu and was the person whom Blue secretly entrusted the Rainbow and Silver Wings with several years ago.

At that same moment, Yellow also recalls the name of the red haired boy as Silver, who is said to have shared a bitter childhood with Blue training under the Mask of Ice in the past.

Leaving Sneasel on his shoulder and lifting himself off on Murkrow, Silver retrieves his other Pokémon, and hovers over to land straight in front of Yellow. He wants to know why Yellow is there, and the girl, who is surprised by the question, explains that she lives in Viridian. Astonished to hear that, Silver quickly takes out his Pokegear, and checks on the complete profile of all Pokedex holders which Blue gave him. He discovers that the girl indeed hails from Viridian, and is nicknamed Yellow of the Viridian Forest. But then he also reads that she is actually one year older than he is, and gives her a quizzical look, which makes Yellow wonder if something is wrong.

Yellow then asks why Silver has come to Viridian, and the boy reveals that he is there to search for his roots. All his life, he has no idea where he comes from and knows nothing about his family. Yet following some extensive investigations across the land, he has recently found clues that led him to Viridian, and has thus dropped by to see if he could learn anything about his past.

At a very young age, Silver and his Sneasel were kidnapped and brought to a place where he spent the majority of his childhood training under the evil masked man. Blue, in fact, had the same unfortunate fate. However, with persistance and endless searching, the girl has finally located her parents at the Sevii Islands, and managed to make contact with them not too long ago.

Silver remarks that Blue is most likely enjoying the long awaited reunion with her parents right now, and feels truly happy for her, who has treated him like a big sister all these years. Seeing the success of Blue, Silver believes that with enough effort and luck, he might just be able to achieve the same thing as well. But then he puts on a bitter smile, and admits that he is fully aware of how much more difficult it will be in his case, since he doesn't even know where his home is.

Having heard Silver's story, Yellow grins that she could perhaps help him out a little. She reaches out to pat Sneasel on the head, and says while Silver might not have remembered much about his childhood, there is a chance that Sneasel does, as it was kidnapped together with him. She explains that she is able to read the minds of Pokémon, but Silver simply shakes his head, and states as a matter of fact that it would not work.

He reveals that he has in fact sought help from Lance, who possesses the same ability as Yellow, but even this dragon master of the Kanto Elite 4 failed to retrieve anything that happened before the kidnapping from Sneasel's memories, and believed that the incident was too traumatic for Sneasel, thus causing it to lock out part of its memory.

Yellow feels sorry to hear that, but suddenly senses a powerful emotion coming from Sneasel. She alerts Silver that the Pokémon seems to be reacting to something, and wonders if Viridian could really be a key to Silver's past, and the sight of this place is triggering some lost memories in its mind. The girl quickly takes out her sketchbook and pencil, and wants Sneasel to focus its thoughts just for a while. Using her mind-reading ability, Yellow tries to draw out what Sneasel is seeing in its visions, and gasps in shock when she realizes what it is.

Without another word, the girl hurries back into the Viridian Gym, and Silver quickly trails after her, baffled about what is going on. Yellow stops in front of the half broken statue of the previous Viridian gymleader, and after looking back and forth several times between the concrete figure and what she drew on the sketchbook, mutters in disbelief that the statue is what appeared on Sneasel's mind.

Back at the Trainer Tower on Seven Island, Prof. Oak and Blue are running down the stairs and across corridors while a number of Deoxys-Divides chase after them. Blue wonders what Oak meant when he said retrieving their Pokedexes, and the professor reveals that the three stolen devices of the Pallet trainers are still inside a research room on that floor.

One of the Deoxys-Divides morphs its tentacles into a hand, and attempts to grab Oak, but Blue sends out Jiggly just in time, and the pink balloon Pokémon inflates itself to block the entire corridor, bouncing back all the humanoid creatures with its elastic body. While Jiggly halts the advance of their pursuers, Oak and Blue locate the research room, and enter to find the three Pokedexes inside a glass dome.

Oak remarks that Team Rocket has actually been after Deoxys for some time, but it apparently wasn't easy to capture to being. The reason why they attacked him at the Science Lab and snatched the Pokedexes is because the devices hold the valuable records of Red, Green and Blue previous battles, and the data will help them tremendously in figuring out a way to catch Deoxys. In fact, after Team Rocket learnt of how the Pokedexes work, they made their own machines which have identical functions, with the additional feature of battle recording, which incorporates a unique formula they invented themselves to accurately calculate the HP and attack power of Pokémon.

Blue recalls hearing from the others about the enemy holding such mysterious black machines during Red's battle with Deoxys, and Oak states that the TR secret agents deliberately created the chance for Red to face the creature, because they needed to collect the most in-depth data about the Pokémon's battling styles in order to prepare for capturing it.

However, Oak points out, it is time for them to retaliate. He takes off his lab coat and rips off its underside, revealing the three brand new machines in red. Blue realizes that they are the new Pokedexes, and is surprised that Oak has been carrying them around with him all this time. Oak explains that they are still empty shells, and they must transfer the data from the old ones to make them functional. Retrieving the old dexes from the glass dome, the professor wastes no time begins the data transfer by using a connection cord.

Just then, Jiggly finally loses its ground against the Deoxys-Divides, and deflates back into its original size. The humanoid creatures immediately swarm into the research room, and two of them fire off a DNA-shaped laser beam towards Blue and Oak. Fortunately, Blue is prepared and calls out Ditty, who transforms into a giant umbrella and shields off the attacks. Oak hollers that the transfer will take a little while, and urges Blue to hold them back as long as she can. The girl then sends out Bull to join in the fight, and the Snubbull quickly delivers a body slam to knock back its foes.

However, one of the Deoxys-Divides manages to get past Blue's Pokémon, and stabs its tentacles into one of the old Pokedexes. Blue cries in horror that the device is destroyed, but Oak tells her not to worry, and says the data transfer has been complete for that dex. Soon, all three new Pokedexes have been updated with the old ones' records, and Oak says the final step will require the items he placed in Blue's custody.

Blue has no idea what Oak is talking about, and the professor wonders if she has opened up the envelope he left together with her Fame Checker. Blue realizes that Oak is referring to the three mysterious chip-like items she found in them, and quickly reaches into her bag for them. Oak explains that they are called the DEX version IV, which are the most vital parts for upgrading the Pokedexes.

Blue watches as Oak fits the small discs into the three new machines, each with the respective names of Red, Green and Blue printed on them, and wonders why he placed such important items under her care. Oak grins that it is because Blue is the craftiestout of the three, and the girl quickly sweatdrops at the supposed compliment. Oak giggles that if he gave the chips to either Red or Green, the two hot-blooded boys will very likely expose them to the enemy due to their blunted words and actions. But with Blue's wittiness, he is certain that they will be very safe and out of sight.

Oak remarks that when Team Rocket unexpectedly showed up to kidnap him at Pallet Town, the DEX. IV chips were the only things that he could not afford to be snatched by them. While he inserted the Tri-passes into the envelopes of Red and Green on top, he secretly slipped the chips into Blue's envelope which was at the bottom. Once the chips were not not with him, Team Rocket would have no way of learning of their existence.

The truth is, once the DEX.IV chip upgrades the Pokedex into the national dex version, the device would be capable of registering information on Pokémon most people, especially Team Rocket, still do not know of. These data involve powerful Pokémon which could potentially plant the seeds of new conspiracies and evil schemes, and thus must be kept under top security.

Just then, the top corner buttons of all three new Pokedexes blink with a green light, signifying a successful upgrade, and Oak exclaims in excitement that the newest version of Pokedexes are now complete.

Meanwhile, Red's Saur and Green's Charizard are having a hard time fighting down the Deoxys-Divides. Although the humanoid creatures are knocked motionless everytime they are blasted down, they recover again after a brief moment, and are simply impossible to destroy. Green grunts that they are fighting a pointless battle, since the Deoxys-Divides are just divisions of Deoxys, and cannot be completely eradicated until the real Deoxys is taken out. He rationalizes that the real Deoxys must be controlling them from somewhere nearby, and states that they must locate it as soon as possible.

Red tries to think over what Green says, but feels that something isn't quite right. Just then, he hears Mewtwo's voice in his head crying out in agony, and turns around to see that the genetic Pokémon is still unable to break out from its white armour while its full power is suppressed by the device. The tower's mother computer 'r' chuckles that it is interesting to see a Pokémon as powerful as Mewtwo trapped by the M2 Bind, its specially designed restrainer, and Red grits his teeth in frustration.

Mewtwo tells Red not to worry as 'r' will not be able to hear its telepathy, and says it agrees with Green's point of view that the only way to deal with the Deoxys-Divides to is find Deoxys and defeat it. Red states that he fully understands it, but they cannot leave when Mewtwo is still trapped to 'r' by the M2 Bind. Mewtwo says they will have to help it break the restrainer with their Pokémon attacks, but Red finds it ridiculous, as 'r' has reiterated many times that Pokémon attacks will not work.

However, Mewtwo explains that it does not really mean the device cannot be destroyed by Pokémon attacks, but rather, by destroying it, the powerful force will kill Mewtwo itself as well. It tells Red that he knows of the three ultimate attacks, frenzyplant, blastburn and hydrocannon they have learnt from Brinca, and Red immediately calls it silly when he realizes what Mewtwo is suggesting. The boy states that the attacks possess deadly powers and Mewtwo will definitely not be able to survive, but the genetic Pokémon has come up with a strategy that might work.

Mewtwo asks Red to recall that fire is a Pokémon type weak to water, while water is weak to grass, and grass is weak to fire. The three elemental types form a perfect triangular relationship, weak and strong against each other simultaneously and able to cancel out each other's power. Red starts to understand what Mewtwo is saying, and Mewtwo proposes that by firing the three attacks from three different directions at the same time, their combined power will blow apart the M2 Bind, but cancel out each other before itself is hit. However, it is still a very dangerous move because the timing and angle of the three attacks must be absolutely right.

Red hesitates over Mewtwo's suggestion, but Mewtwo points out that they have no other choices. After another moment of thought, Red makes up his mind and agrees to the plan, and declares that they shall wipe out the Deoxys-Divides together, then head off to chase after Deoxys. Green is surprised to hear that Deoxys isn't at the Trainer Tower currently, and wonders how Red knows about it. Red explains that he gets an uneasy sensation inside him everytime Deoxys appears. However, he doesn't feel it right now, and its absence indicates that the creature is not around. In fact, he suspects that Giovanni has taken it somewhere else after occupying them with the Deoxys-Divides.

Up in the air above the oceans, the Beast Warrior Trio bow to their boss, and Giovanni thanks them once again for their hard work. He walks over to Deoxys, who is standing in front of an electronic world map, and says it is time for it to demonstrate its unique power. Reaching into his pocket for a small hankerchief which has a name sewn on the corner, the man wants Deoxys to find out if the owner of the item is still alive, and if he still is, where he would be right now.

The aqua green and orange creature holds the hankerchief with its tentacles, and instantly gets a vision of a young boy with red hair. Its eyes widen with a glow, and its scope of view gradually expands panoramically until it sees the world as a crystal blue globe. It then swiftly zooms in on a city surrounded by a lush forest, and without warning, shoots out its tentacle to pinpoint the Viridian City from the electronic world map.

Giovanni exclaims in disbelief that the person he seeks is currently at Viridian, his very own home town, and feels grateful that Deoxys's special psychic vision ability lives up to his expectations. Jagura gets an uneasy feeling as sees the TR leader's exhiliration, and steals at glance at the photo he stuffed in his back pocket. With a new goal set, Giovanni announces that Viridian City will be their next destination, and the TR battle airship begins its flight back towards the mainland of Kanto…

Thanks To Coronis For Writing this for us