The third part of the manga was never printed in CoroCoro Comics; instead, it premiered in the graphic novel version.

Chapter Three
Fureaeru Nakama...!! ("Getting in Contact with a Friend")

Satoshi charges through the Shadow Clones, telling them all that they're not the real enemy.  Everyone figures out that the Shadow Clones are after the Crystal Body, so Ryuu calls out his Bashamo and Hitomi calls out her Metagross to help as Haruno helplessly cowers in the distance.  Suddenly, a Shadow Deoxys appears in front of Haruno, causing him to scream.  Haruno starts to run away, but he is stopped by Toh'i's pleas.  The young boy tells Haruno that he needs to use the Crystal Body to awaken a second Deoxys, so the lab assistant begrudgedly obeys.  He places the Crystal Body into a machine, and after it glows and clatters for a bit, a second Deoxys is formed!!  With the appearance of a real Deoxys, all the Shadow Deoxys vanish into thin air as Toh'i tells the new Deoxys that he's his friend from before.  The new Deoxys smiles happily.

Nearby, the machine that was just used to revive the second Deoxys starts to react with all the blocks it's sitting on.  Suddenly, one of the blocks is activated, and it looks really angry!  Soon, the rest of the blocks come to life and start climbing up the buildings in the city, smothering them in a sea of blocks!  Haruno, speaking to himself, says that the blocks are the city's defense mechanisms, the Blobo.  He then realizes that his machine must have activated their defensive mode, causing them to wreak havoc!  As the Blobo continue spreading over the city, Rayquaza, who's still squeezing Deoxys, takes notice of all the blocks.  Suddenly, a number of blocks start shooting themselves at the two fighting pokemon!!  As Rayquaza is being buffeted by the incoming blocks, it loosens its grip on Deoxys, allowing the DNA pokemon to escape.  However, rather than run away, the pokemon from space launches into Defense Form and shields Rayquaza from the Blobo!  Rayquaza takes notice.

Below, the blocks are getting out of hand as Ryuu and Hitomi are swallowed up by the thousands of Blobo.  Toh'i, Plusle, and Gonbe start to be overtaken as well, so Satoshi, Pikachu, and the new Deoxys rushes over to help.  As Rayquaza is being engulfed by the blocks above, the blocks below form a sort of jail cell around everyone, closing everyone off from the outside world.  Satoshi tries to tackle his way out of the new "room," but it's no use.  Satoshi then notices Gonbe eating a hot dog, and he comments on the fact that Gonbe eats a lot despite the fact that it doesn't move so much.  Suddenly, the little pokemon starts to glow, and, as everyone watches, it evolves into Kabigon!  The pokemon's sudden increase in size causes the room to burst open, freeing everyone. 

Now that everyone's free, Satoshi notices that the Blobo are still going and wonders how to stop them.  Just then, Haruno approaches the young boys and gives them a Passport.  He informs them that if they can get the chief robot to read the card, the Blobo will stop their rampage and everything will return to normal.  Satoshi approaches the tower covered in Blobo and, not knowing which one is the chief robot, begins showing the card to random blocks.  Satoshi exclaims that there are too many of them to know, but luckily for him Pikachu is able to spot the one Blobo that's different from the others.  Satoshi starts climbing up to its location, but he slips on his way up!  It looks like it's the end for Satoshi when Toh'i, riding on Deoxys, flies in and swoops Satoshi up!  Deoxys then flies Satoshi up to the chief robot, where the young trainer from Masara Town gives the Blobo the Passport to read.  The robot accepts it (you can tell because its angry face turns into a happy face), and as soon as it does the other Blobo start to fall. 

As the blocks continue to topple lifelessly, both Ryuu and Hitomi can be seen emerging from the pile of blocks, seemingly OK.  We also see the first Deoxys flying out of the pile of blocks, carrying a wounded Rayquaza!  The dragon pokemon soon wakes up, though, as everyone who was taken away by the Shadow Deoxys are able to escape from their prison.  As Haruno walks off without a word, everybody eagerly reunites with all their friends.  Toh'i thanks Deoxys for saving him and then surprises everyone by patting Plusle and Minun on the head.  Toh'i's fear of pokemon seems to have subsided, and as he hugs his new friends, everyone is reminded that they're not alone.