The two young men slowly make their way to the cave opening which leads to the secret laboratory, and joyfully announce their arrival as they enter through the big metal doors. Inside, the Cinnabar Gymleader Blaine turns around on his seat, and greets his two old acquaintance merrily. He remarks that they have arrived earlier than he expected, otherwise he would have gone to welcome them outside personally.

Bozz grins that they know each other too well for that kind of formality, and notices a thick photo album on Blaine's working desk. He wonders what it is, and Blaine explains that they are very old photos of his. One photo shows Blaine in khaki shirt and shorts, standing deep inside a jungle next to an older man named Prof. Fuji as stated in the caption, dated 5 July. Subsequent photos follow a chronological order and seem to narrate a series of events.

Blaine laughs that he felt a sudden urge to revisit old memories after Bozz and William told him that they would be coming for a visit, and starts explaining about the photos. But then, a sharp pain suddenly courses through his right wrist, and Bozz quickly inquires if he is alright. Blaine winces that although he is no longer connected with Mewtwo, the old wound on his right wrist still serves as a memoir which would probably never go away. Since the day before, he has been experiencing a progressive pain there, and he figures that Mewtwo must somehow be feeling unsettled.

However, Blaine states that he has never seen or met anything that could cause such a profound effect on the psychic mutant. Right now, the only possibility he could think of is that, the elusive phantom Pokémon Mew who have not been seen for so long, whose DNA basis Mewtwo was created from, is for some unknown reason coming back to Kanto again.

Meanwhile, at the midair battle stadium on the TR battle airship, Giovanni gasps with surprise as Red charges towards him. The boy then does a somersault to leap over Giovanni, and darts straight for the device the man placed on the side of the stairs earlier, which he rationalized must be something used to control the light beams coming from the four poles surrounding the stadium.

Giovanni immediately realizes that Red is aiming for the battle airship's master remote control and quickly turns around, but the boy has already gotten hold of it successfully, and is starting to narrow the light beams towards Mewtwo. Deoxys is stunned momentarily by the unexpected happenings, but then swiftly reacts by sending out its four tentacles to grab Red from behind, trying to snatch the device back. However, the pyramid of light beams have fully closed in on Mewtwo, essentially creating an energy barrier around it.

Red hollers that the barrier will provide a temporary protection zone, and tells Mewtwo to make use of the chance to recover itself within it while Deoxys is busy restraining him. Giovanni spats that he was expecting a tackle from Red and never would have thought that he was targetting the remote, but Red says the entire battle airship is their current battle field, and it was Giovanni himself who taught him to utilize everything within the battle field to one's advantage.

Struggling against Deoxys's tentacles, Red urges Mewtwo to hurry up before he loses the remote control back to their foe. Inside the pyramidal energy shield, Mewtwo weakly nods and wills its body to move, telling itself that all it needs is to fire another shot. It then snaps its eyes wide open, and begins glowing with a blinding light as it uses recover to heal itself. With its powers restored, it begins creating a sphere of energy in its left hand, while Red proceeds to lift the light beams away with the remote control.

The boy then assures Mewtwo not to worry about Deoxys's aurora camouflage, since he is able to tell its real form from his close proximity. He hollers that the creature is still currently in its attack form, which its defense is weakest, and orders Mewtwo to strike. However, Giovanni quickly commands Deoxys to fly, and the DNA Pokémon rapidly transforms into its speed form, taking Red along with it as it blasts off into the air and circles around with the speed of a jet.

Giovanni smirks that Mewtwo will have a higher chance to hurt Red instead if it attacks while its opponent is moving so fast, and the psychic mutant begins to hesitate. It knows that the man is right, and grunts in frustration, but Red reassures Mewtwo that it will be alright, and urges it to fire another attack at Deoxys's core. Yet, Mewtwo remains doubtful, and Red yells at the top of his lungs with an annoyed tone that it is a trainer's command.

In that instant, Deoxys morphs into its defense form, just as Mewtwo decides to take a risk and hurls the sphere out into a psychic blast. The attack narrowly avoids Red, and courses straight through the crystalline organ on Deoxys's chest. The DNA Pokémon immediately lets out a shriek before tumbling onto the ground, freeing Red who lands with a crash next to it. While Red pants heavily to catch his breath on the floor, Giovanni stares with a stunned expression at the fallen creature from space, knowing that he has lost.

The TR leader walks up to Deoxys, and demands to know why it morphed into its defense form without an order, which although has better defence in terms of status, lacks the speed it needs to distract the enemy with. However, as Giovanni takes a closer look at Deoxys, he notices that something is wrong. The Pokémon spasms in agony while it changes forms uncontrollably on the floor, but instead of all four forms, it is only shifting between its attack and defense forms.

The man gasps with realization that it isn't simply suffering from a direct blow towards it core, but seems to have lost the ability to morph into its normal and speed forms. Fear washes across his mind as he knows that there is only one possible explanation for that.

Deoxys's form change ability lies in its high susceptibility to its environment, and its normal and speed forms are exclusive to Hoenn's climate. In order to enable its access to these apperances in Kanto, they have used the combined energies of the Ruby and Sapphire stone plates on Five Island to recreate the Hoenn climate. Yet, this energy seems to have disappeared now, which means that someone has taken away the stone plates from their amplifiers on Five Island. Grinding his fist in anger, Giovanni wonders who the culprits are.

At the Team Rocket Warehouse on Five Island, Bill and Celio have successfully taken out all the TR grunts and tied them up. While his Exeggcutor and Vulpix guard them close, Bill holds onto the Ruby and Sapphire stone plates which he just removed from the energy amplifier machine, and feels grateful that he has finally located what he sought.

From the monitor screen of Team Rocket's computers, Celio sees that the energy waves created by the two stone plates have completely dissipated, and exclaims that the artificial Hoenn environment recreated in Kanto is finally dispersed. Bill remarks that what Lanette and Bridgette suggested was true afterall, and Celio rejoices that they could now limit Deoxys's form change ability.

Back on the TR battle airship, Yellow wanders around with Ratty and Freesk, and starts to get lost inside the giant aircraft. She wonders where Silver could be, and soon sees a door ahead of her. She decides to try her luck, and jumps with shock when she opens it to find the mid-air battle stadium where Mewtwo and Deoxys are battling. She calls out with a stuttering voice when she spots Red, and rushes down the stairs to meet him. Red is equally surprised to see Yellow, and wonders why she is there.

Yellow begins to explain about how the secret agents of Team Rocket kidnapped Silver in front of the Viridian Gym, and what they said about the leader of Team Rocket being Silver's father. But then, she hears a voice in her head, and turns around to see Deoxys trembling and struggling on the ground. Staring at the aqua green and orange creature, she wants to know if it was the one who just spoke to her…

Thanks To Coronis For Writing this for us