This second part of the manga was originally included in CoroCoro Comics #315 (July 2004).

Chapter Two
Shougeki Hakkaku!  Suishoutai no Nazo ("The Shocking Revelation!  The Riddle of the Crystal Body")

An announcement over LaRousse City's PA system says that everyone needs to evacuate because of the battle.  As the announcement is being made, everyone runs for their life.  The battle between the legendary pokemon continue as Deoxys transforms into its Attack Form.  The DNA pokemon charges up an energy attack and unleashes it on Rayquaza.  Meanwhile, the people on the street are still panicking as the PA system assures everyone that this is not a drill. 

Among the people running is Toh'i, who wonders why Deoxys is still alive.  As he's escaping, he comes across a distressed-looking Plusle.  Toh'i is scared by the sight of the pokemon, but he soon forgets about his fear as he listens its cries of help.  He is able to determine that Plusle is upset because its friend is trapped inside a garbage can, so Toh'i decides to help it out.  He removes the lid only to be greeted by an ecstatic Minun!  Toh'i is scared again, and as he tries to get away from the pokemon Gonbe emerges from the garbage can.  When Toh'i notices Gonbe, the young boy faints.  Satoshi and the gang arrive to find the unconscious Toh'i, so Satoshi tries to snap the young boy out of it.  Toh'i wakes up and tells Satoshi that he doesn't need his help as Gonbe is seen in the background, picking up some trash.  As Haruka, Takeshi, Masato, Shouta, Ryuu, an unknown woman and two children arrive, Satoshi tells Toh'i that he needs to hurry up and get away.  Before Toh'i gets a chance to obey, a giant beam from the battle above crashes down on the ground nearby, scaring the bezeesus out of everyone.  Everyone wonders where they can run to, and Toh'i tells everyone to follow him. 

The group is lead to the pyramid-shaped botanical garden that Toh'i went to before.  As everyone waits for Toh'i to open the door, the young boy comments that the door's card reader isn't working.  Shouta steps up and says that he'll take care of it and proceeds to pry the doors open with his bare hands.  Everyone cheers Shouta as Ryuu looks over at Satoshi.  He comments on the fact that Satoshi is still in LaRousse City, saying that he thought he would have left after his humiliating defeat at the Battle Tower.  Satoshi gets angry and demands a rematch, and Haruka has to step up and tell Satoshi that now isn't the time.  The two little girls from before, who happen to be twins, boast that their big brother Ryuu is too strong to lose to Satoshi.  Satoshi asks them who they are, and the woman with glasses respond that they're Ryuu's younger sisters, Audrey and Catherine.  She then introduces herself as Hitomi.  Takeshi does his usual fall for the beautiful girl routine, and Masato responds by pulling him away by his ear. 

Later, Ryuu asks what they should do since it's so dangerous outside.  Hitomi, who has her laptop with her, begins to look up information on the DNA pokemon.  She can't find any data on the pokemon, and a frustrated Shouta asks her to try harder as Gonbe can be seen sleeping in the background.  Satoshi notices Toh'i looking sad, so he asks him what he knows about the pokemon.  Everyone stops what they're doing and turns around to listen to Toh'i's answer, and Rondo-Hakase's son looks up at the battling pokemon in the sky.  Toh'i tells everyone that Deoxys is a pokemon from space, much to the surprise of everyone listening (except for the sleeping Gonbe).  Toh'i says that four years ago, a meteorite crashed on the planet.  From the meteorite was born a pokemon, a pokemon whom Rondo-Hakase would give the name "Deoxys."  The pokemon was a devil who invaded the territory of the ozone pokemon Rayquaza, so a battle broke out.  The two started fighting, and an attack from Rayquaza disintegrated Deoxys into very small pieces, killing it.  Ryuu doesn't believe the story, saying that it's ridiculous, and Shouta tells Toh'i not to insult them like that.  He asks the young boy why Deoxys is alive now if it supposedly died four years ago, and all Toh'i can do is solemnly admit that he doesn't know. 

Above the botanical garden, Deoxys begins to make Shadow Copies of itself.  The copies spot the residents of LaRousse City hiding behind trees and whatnot, fearfully looking up at the battling pokemon.  The Shadow Deoxys swoop down and begin grabbing the people, taking them away to some unknown location. 

Back in the botanical garden, everyone is listening to a news broadcast through Hitomi's computer.  The reporter announces that there is a barrier around the city and that nobody can get in or out.  It also reports that Deoxys has made Shadow Copies of itself who are going around snatching up the residents of LaRousse City.  Hitomi shuts the computer off as Shouta worries about being confined in the city.  As a Shadow Deoxys can be seen approaching in the background, Audrey and Catherine begin to cry.  Suddenly, a Shadow Deoxys crashes through the glass roof of the garden, surprising everyone.  Toh'i recognizes the pokemon and yells for everyone to run, but the Shadow Deoxys begin swooping toward the humans.  Shouta calls his Kamex out and commands it to use Hydro Pump.  The attack doesn't affect the Shadow Copy, and as Shouta wonders why it didn't work another Shadow Copy snatches both Shouta and his Kamex from behind.  They carry the large trainer out through the hole in the ceiling, much to Ryuu's dismay.  Ryuu is now upset, so he calls out his Bashamo to use its Fire Punch attack on one of the Shadow Copies.  Satoshi calls out his Pikachu to use Thunderbolt, Hitomi calls on Metagross to use its Comet Punch attack, and the twins call on Ametama and Amemoth to use Bubble Beam.  As the pokemon occupy the Shadow Deoxys, Satoshi tells everyone to run as Ryuu asks Toh'i if there's an emergency exit anywhere.  Suddenly, Takeshi notices that his Monster Ball won't open, and the others confirm that theirs won't open either. 

The Shadow Deoxys close in again, so Toh'i begins running again.  Ryuu's Bashamo attacks the Shadow Clone to protect Toh'i as he tells everyone to go on without him.  Haruka objects as Ryuu tells her to take care of his younger sisters for him.  Meanwhile, Takeshi is busy trying to wake up Gonbe, who is still sleeping after all this time.  Back at the battle, Bashamo uses its Sky Upper attack to buy the gang some time to find the exit.  Once they arrive, Haruka and the others tell Satoshi to make a run for it, and they reply by telling Haruka and the others to go on without them.  Just then, Gonbe emits a giant yawn (which is shown as a large beam) from its mouth.  The beam, which spreads over the entire area of the garden, disintegrates all of the Shadow Deoxys, enabling Satoshi and the others to safely get away.

Meanwhile, in Rondo-Hakase's lab, the doctor lies unconscious as Haruno looks over him.  Haruno, who has a taser in his hand, thanks the unconscious Rondo-Hakase for all the work he's done and says that he'll take over his research.  Haruno then looks over at the Crystal Body and dreams about how it will give him wealth and reverence, and how his presentation of the essence of Deoxys will revolutionize the Pokemon World.  Suddenly, a knock is heard on the door, startling Haruno.  It's Toh'i, and he asks somebody to let him in so that he can see his father.  Outside, Toh'i explains to the others that they're right outside his father's lab, and that the lab itself is actually buried underneath the botanical garden.  Soon, Haruno opens the door and lets the kids in.  Rondo-Hakase is nowhere to be found, so it's assumed that Haruno quickly hid the doctor.  Toh'i asks Haruno where his father is, and he tells him that Rondo-Hakase is outside, looking for him.  Toh'i worries because it's so dangerous outside, but Haruno assures Toh'i that his father will be OK.  Satoshi decides to go out and look for the doctor, but Ryuu stops him before he can get too far.  Ryuu believes that if Satoshi leaves, he'll put everyone else in the lab at risk, so Satoshi decides to stay put and wait for Rondo-Hakase to return.

It's nighttime now, and the doctor still hasn't shown up yet.  Audrey and Catherine complain about being tired and hungry, so Ryuu tries to comfort them by asking them to be a little more patient.  Gonbe walks up to the twins with a sandwich in its hands, and the twins assume that the pokemon's brought it for them.  Wrong!  Gonbe quickly gobbles up the sandwich in front of their faces, causing Ryuu's younger sisters to start crying.  Satoshi says that he's going to go and search for some food, but Ryuu reminds him of how dangerous it is outside.  Satoshi doesn't listen this time and begins to run outside anyway, so Ryuu and the others decide to follow.

Outside, the Shadow Deoxys can be seen flying around as if on patrol.  Satoshi and the others stay low to avoid being seen, and after the Shadow Clones pass by a plan is devised.  Everyone is told to grab some food and water and then return quickly, and with that the gang splits up.  Satoshi, Takeshi, and Pikachu find a hot dog vendor, but the cart is closed off.  Satoshi tells Pikachu to give it a Thunderbolt, and after the electric mouse obeys, the robotic vendor starts up as it begins playing music.  Hot dogs begin to fall out of the machine, so Takeshi grabs as many as he can carry.  Suddenly, Takeshi tackles Satoshi to the ground and tells him to be quiet as a group of Shadow Clones pass overhead.  The two trainers and Pikachu hide behind the robotic vendor, but the machine's music continues to play.  The Shadow Deoxys hear the music and approach the vendor, and a nervous Satoshi and Takeshi think they're done for.  Suddenly, Toh'i, Plusle, and Minun appear from the other side, unaware of the Shadow Deoxys' presence.  The Shadow Clones swoop down toward Rondo-Hakase's son, but Plusle and Minun protect him by using a combined electric attack.  Just then, one of the Shadow Deoxys snatches Minun and Toh'i!  Satoshi jumps on the Shadow Deoxys that has Toh'i and bites its arm, causing it to drop the young boy.  Satoshi asks if he's OK as Pikachu attacks the other Shadow Clones, but there are too many for the group to take on.  Satoshi tells everyone to run, but Toh'i is worried about Minun.  Takeshi tells him that they need to worry about getting out of there first, so the group runs away.  They reach a building with an open window, so they quickly jump inside to hide.  The Deoxys clones pass by without noticing the young trainers, so they can relax for a while.  Toh'i notices that Plusle is upset about losing its friend, so he approaches the pokemon to pat it on the head.  However, his body freezes up with fear and he's unable to pet the electric pokemon, so he apologizes to Plusle.  Elsewhere in the building, Pikachu notices a supply of bottled water just sitting there in the building, causing everyone to cheer.

Later on, everyone has managed to make their way back to the lab.  Everyone's eating the vending machine hot dogs and comment on how great they taste.  Ryuu shows Satoshi a news report on Hitomi's computer that says that the captured people (which include Musashi, Kojirou, Nyasu, and...Koduck?) are all being brought to an unknown location.  Takeshi wonders why Deoxys is collecting all the people in one place, and suddenly Rondo-Hakase's voice is heard.  The doctor, who has obviously just come to, crawls out of a closet and tells the trainers that Deoxys is searching for a friend.  He then asks everyone where Haruno is, and they inform him that he went outside (we never actually see Haruno leave, so we can only assume that he left off-camera).  Rondo-Hakase looks over and notices that the Crystal Body is missing, so he tells everyone that Deoxys is also searching for the Crystal Body.  Toh'i asks what it is, and Rondo-Hakase tells him that it's another Deoxys--that Deoxys has two bodies!!  Rondo-Hakase tells the group that Haruno and he were researching regeneration and that the Crystal Body was the key to their research.  Masato tells the doctor that Haruno left with the Crystal Body, and Ryuu guesses that the research that took it away from Deoxys is what caused the DNA pokemon to go on the rampage that it's on now. 

Suddenly, the mysterious light that talked to Toh'i in the botanical garden before appears again and talks to the young boy.  Toh'i tells everyone that it's his friend, and the light reveals itself as the other Deoxys.  Toh'i tells his father that he thinks that the Crystal Body is alive and rushes off to go search for it.  Everyone else follows.

In a remote area of LaRousse City, we see Haruno frantically running with a box in his arms.  A beam from the battle above crashes down to earth, disorientating Haruno and causing him to drop the box.  The force of the fall causes the box to open, and the round Crystal Body rolls out.  Rubble (mostly the city's Block Robots) from the explosion begins falling on Haruno, and Rondo-Hakase's assistant is buried under it all.  Above, the battle between Deoxys and Rayquaza is still going strong. Rayquaza starts to wrap its body around the DNA pokemon and squeezes tightly, immobilizing Deoxys.

Toh'i and the others are running along outside, being guided by the light in Toh'i's hand.  Toh'i understands why Deoxys wouldn't want to be alone and knows how it feels to be lonely, and he vows to bring Deoxys a friend.  Everyone else vows to help out and to stop the fighting between Deoxys and Rayquaza.  Close by, Haruno emerges from the rubble, cursing the trouble the Crystal Body has brought him.  The confused assistant wonders where the Crystal Body is, but he calmly exclaims that he can quickly find out.  He gets out a remote control and presses a button that causes the Crystal Body, which hadn't rolled too far away, to emit a blinding light.  Above, Deoxys, who's still being squeezed by Rayquaza, notices the light and gets an angry look on its face.  Back on the ground, the light in Toh'i's hand begins to float toward the light emitted from the Crystal Body, so Satoshi starts to cheer that they've found it.  Ryuu wonders what's causing it to glow the way it is, so everyone goes down to investigate.  They find Haruno, who claims that the Crystal Body is his.  The assistant reaches for the orb and is about to grab it when a swarm of Shadow Deoxys appear and surround him.  Ryuu figures that the pokemon must be after the Crystal Body, and Satoshi says that he'll help Haruno out this time!!