This first part of the manga was originally included in CoroCoro Comics #314 (June 2004).

Note:  The following summaries will be taken down and replaced with less detailed summaries if Viz ever picks the series up for distribution in the United States.

Chapter One
Uchuu kara Kita Pokemon!! ("The Pokemon that Came from Space!!")

In an icy field, the DNA pokemon Deoxys and the ozone pokemon Rayquaza are in the middle of a terrific conflict.  Judging by the ruined wasteland around them, the pokemon have been duking it out for quite a while now.  Apparently, Deoxys is trying to protect a crystal object in the ice field, and it seems that it's been successful so far.  After an intense stare-off, Rayquaza fires a Hyper Beam at Deoxys.  The beam hits Deoxys' right arm, slicing it right off!  However, Deoxys merely looks down at what's left of its arm and watches as it grows back!  Rayquaza looks surprised as Deoxys prepares a counterattack.  However, Rayquaza fires another Hyper Beam, only this time it seems to destroy Deoxys' entire body!!

Suddenly, a young boy screams in terror.  The young boy, Toh'i, awakens in a laboratory in the High Tech LaRousse City.  The battle between Deoxys and Rayquaza was a nightmare that Toh'i was having, and his sudden jolt into consciousness alerts Rondo-Hakase, his father, and his lab assistant, Haruno.  Haruno asks Toh'i what he was dreaming about, and he informs him that he was dreaming about the incident that occurred four years before.  Haruno tellsToh'i that it was just a dream, and that he shouldn't worry because Deoxys is dead. 

Toh'i seems doubtful, but Haruno doesn't have time to reassure the boy any further.  He is summoned by Rondo-Hakase to activate a laser device aimed at a "Crystal Body," the crystal object that Deoxys was trying to protect four years before.  The laser is fired, but nothing seems to happen.  Haruno comments that the Crystal Body does seem to glow when a laser is aimed at it, but other than that there doesn't seem to be any other change.  Rondo-Hakase seems determined to figure out the Crystal Body's secrets, confident that whatever he uncovers will revolutionize the Pokemon World.  As the professor continues admiring the Crystal Body, Toh'i senses that the mysterious object is alive...

Out in the city, a subway arrives, and out of it comes Satoshi, Takeshi, Haruka, and Masato!  After a robot dog/block robot gives everyone a Passport, Satoshi immediately finds what he came to the city to see--the Battle Tower!  Masato wonders what's so great about the Battle Tower, and Takeshi explains that the Battle Tower is where the strongest trainers from all over gather to battle.  As Satoshi happily walks toward the tower, a shadowy figure sneaks up from behind and steals his hat!  The thief ends up being Plusle and its friend, Minun!  Satoshi begins chasing the two mice pokemon, and when he thinks he gets close enough he dives for Plusle.  However, he seems to have misjudged the distance between him and the electric pokemon since he crashes into a trash can!  Satoshi now has garbage all over him, which only makes him even more angry.  He continues chasing them right to the Battle Tower as a Gonbe appears to pick up the trash can that Satoshi knocked over.  Takeshi and the others follow Satoshi into the Battle Tower.

Further inside the Tower, Satoshi's chase brings him to a library.  He seems to have lost the pokemon, so he decides to ask for help.  He spots Toh'i sitting at a desk in the library, so he approaches the young boy and asks him for help.  However, Toh'i seems to be afraid of Satoshi's Pikachu, so he simply walks away without saying a word.  Satoshi follows, telling him that a Plusle and a Minun stole his hat.  Toh'i points to the other side of the room, where Satoshi's battered hat can be seen lying amongst rubbage.  As Satoshi cleans off his hat, he swears that he'll get the pokemon back, unaware that they're hiding on a ledge behind him.  Suddenly, Satoshi and Toh'i are approached by a Battle Tower employee who seems to have mistaken the two boys for Battle Tower participants.  He tells them to hurry up as he pushes them onto a platform.

The two boys end up in a giant battle arena.  The referee announces that the battle can start, saying that the first match will be a Tag Battle.  In the blue corner is Satoshi from Masara Town and Toh'i from LaRousse City, while their opponents in the red corner will be Ryuu and Shouta, both from South City.  Takeshi and the others watch on in the audience as the referee asks the trainers to release the pokemon that they'll use for the battle.  After Satoshi chooses his Pikachu, he asks Toh'i what pokemon he'll be using.  However, Toh'i says that he doesn't have any!  As the referee wonders what's wrong with the red corner, Satoshi tells Toh'i that he can use one of his pokemon for the battle.  Toh'i throws the Monster Ball lent to him by Satoshi, and out comes Satoshi's Kortoise.  Ryuu and Shouta have chosen a Bashamo and Kamex, respectively, and soon the battle commences.

Bashamo starts the battle by using a Blaze Kick.  Pikachu jumps to avoid the attack, but Kamex's Hydro Pump nails the little mouse pokemon while it's still in mid-air.  Satoshi scolds Toh'i for not using his Kortoise to help out, but all Toh'i can do is wonder how to battle.  Bashamo uses Fire Punch on Kortoise, and soon after Toh'i falls to his hands and knees and starts screaming.  This doesn't stop the battle, as Kamex hits Pikachu with a Headbutt attack.  Pikachu bounces off Kortoise and lands hard on the ground, causing the referee to call out the poor teamwork that the two trainers in the blue corner are utilizing.  Satoshi looks over at Toh'i and realizes that the young boy can't be of any use, so he decides to finish the battle on his own.  He orders his Kortoise to use Flamethrower, but the turtle pokemon's attack accidentally hits Pikachu instead!  Ryuu smirks and comments on how they had wanted a challenge, so Shouta suggests that they finish the battle.  Bashamo is ordered to use Sky Upper, which knocks out Pikachu and Kortoise.  Ryuu and Shouta are the winners!!

After the battle, Satoshi and his friends look after his fallen pokemon.  Both Pikachu and Kortoise are OK, but they just need a little rest.  Suddenly, Rondo-Hakase bursts into the room, exclaiming his surprise that his son participated in a pokemon battle, but he tells him that he needs to become more skilled with pokemon.  Toh'i then runs off, which bewilders Satoshi.  He asks what his problem is, and Haruno explains that Toh'i doesn't care for pokemon that much.  He says that, four years ago, Toh'i witnessed a scary battle between Deoxys and Rayquaza, and because of that he is frightened of pokemon.  Haruno expresses his desire for Toh'i to be able to interact with pokemon, so Satoshi makes a decision--he'll help Toh'i get over his fear of pokemon!  Using his pokemon friends, Satoshi will bring Toh'i to love pokemon.  Masato, Haruka, and Takeshi all agree to help, so they all agree to split up to find him.  Haruno thanks the kids for their help.

Elsewhere, a pyramid-shaped botanical garden is seen.  Toh'i is seen inside the garden, calling out to an unseen audience.  Suddenly, a sparkle of light appears and floats down to the boy's hands.  Toh'i tells the light about how he participated in a pokemon battle, but that he was unskilled at it.  He then tells the light that he really does like pokemon, but that even though his heart wants to be close to him, his body always locks up in fear whenever he's around one.  Suddenly, Satoshi and Pikachu approach from Toh'i's behind, startling the young boy.  As the light disappears, Satoshi asks who Toh'i was talking to, but Rondo-Hakase's son replies that it's none of his business before running off again.

Meanwhile, across the ocean, the ice in the icy field begins to crack.  After a massive explosion, Deoxys emerges from the rubble and begins flying toward LaRousse City.

Back in the city, Satoshi is chasing Toh'i through the streets.  Pikachu tries to appeal to Toh'i by jumping on his shoulder, but Toh'i responds by smacking the electric mouse pokemon away.  Satoshi kneels down to make sure Pikachu is OK, and as he gets back up he notices a creature on top of  a skyscraper.  He asks whether or not the creature is a pokemon, and when Toh'i looks up, he is able to see that it's Deoxys!!  Toh'i collapses to his hands and knees, screaming that Deoxys is supposed to be dead. 

Back at Rondo-Hakase's laboratory, the professor alerts Haruno that the Crystal Body is glowing.  As Toh'i's father exclaims that he's close to figuring out the Crystal Body's secrets, Haruno seems to be plotting something...

Back in the city, Deoxys notices a beam of light coming from far away.  The light is a Hyper Beam attack, and the DNA pokemon jumps out of the way just in time.  As everyone below runs from the falling rubble, Satoshi notices that Toh'i is frozen like a deer in headlights.  Satoshi grabs the motionless boy and gets him out of the way while Toh'i mutters to himself that this is a nightmare.  Suddenly, another figure appears in the sky, only this time it's Rayquaza!  Satoshi wonders what Rayquaza is doing there, since it's supposed to live in the ozone layer while Toh'i repeats over and over about the nightmare from four years ago.  Above, Rayquaza fires another Hyper Beam, this time hitting Deoxys head-on.  After the smoke clears, everyone notices that Deoxys is in its Defense Form, completely unharmed!!  What can Satoshi do now!?