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It's Starting to Make Sense Now (デオキシス そのルーツ Deoxys's Roots) is the 9th chapter of Pokémon Adventures: Volume 25.
After the battle, Yellow visits Red and translates a shocking message from Deoxys. Sird and Orm appear and as Orm takes Giovanni away from the battlefield, Sird explains the events taking before this crisis happened.
Yellow came to Red and heard Deoxys talking to her. Mewtwo remembers that Yellow can communicate with the Pokémon and heal them. Yellow senses Deoxys is trying to explain them some things, since it is defeated. Yellow senses and translates Deoxys' thoughts, translating "Red... I am you!" Red is shocked and wants to learn more. Giovanni goes to stand up, but Sird decides to do that instead, having Orm take the boss inside the airship. Red and Yellow try to move, but are surrounded by Sird and Orm's Pokémon. Sird goes to explain Deoxys' origin, but Red is aware it came from outer space, mutated from a space virus. Sird thinks Red should be able to understand what she will explain.
From Mossdeep City's research center, a rocket was fired into outer space, and, by coincidence, they found the virus, which mutated into two forms. The forms were attached to the "Grand Meteor", a meteorite, which fell on the planet. The meteorite was found by Professor Cozmo, who found life forms around the meteorite and took it to Mossdeep Research Center. While they learned, through spies, these new Pokémon would be the most powerful Pokémon they know of, a Team Magma member, Courtney, assaulted the lab. Sird came with the grunts and had the tanks with the two Deoxys sealed inside transported inside the airship. They soon learned Deoxys also had the ability to sense distant objects, even beings. Giovanni was aware he could've even used them to search for his son.
They sent the three members - Al, Herry and Ken - to transport the Deoxys to Kanto. However, during the flight, the trio noticed Deoxys' appearances have changed and made notes about their powers. Sird was intrigued, seeing Deoxys' changed forms, depending on the location. Soon enough, one of the Deoxys had destroyed the tank and escaped. Sird was displeased in the trio and went with Giovanni to the hideout. Sird soon learned Deoxys went to Birth Island, while Giovanni believed it went there to awaken itself. In the present, Sird points at the Deoxys, whose name is Organism Number 2. To gain full power, they let Organism Number 2 free for a while, before Giovanni captured it with the Poké Ball. As for Organism Number 1, they set it free to attack Red and his friends, to provoke him, as well as capturing Green's parents.
Red does not see what is this involving him. Sird reminds Red is angry when bad things happen to his friends and becomes furious - and in that fury, Organism Number 2 appeared. Red recalls Deoxys' words "Red... I am you!" and asks Sird if Deoxys was drawn only to him. Sird confirms this, for their only target was Red. They wanted to get him mad to make Deoxys appear and use the black Pokédex to collect data and capture Organism Number 2. Yellow asks what happened to Organism Number 1. Sird replies it was no longer useful for them and disposed of it. Yellow, however, is concerned about Deoxys' words, wondering what it meant that Red was "it".
Silver, elsewhere, wakes up and sees Giovanni, laying unconscious, on the bed.
|Pokémon: Ruby & Sapphire, FireRed & LeafGreen and Emerald|
Ruby & Sapphire arc
|RGB & YL · GS & CR · D&P, PL & HGSS · B&W & B2W2 · X&Y & ORAS · S&M|