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| It's Starting to Make Sense Now
| デオキシス そのルーツ|
|| Team Rocket battleship
It's Starting to Make Sense Now (Japanese: デオキシス そのルーツ Deoxys's Roots) is the 296th round of the Pokémon Adventures manga.
Yellow hears the voice of Deoxys calling out to her. She guesses that Deoxys is trying to tell them something because it's time is up. Using her powers, Yellow tells Red that Deoxys is claiming that it is him. Red asks Deoxys to explain what it means by that. Giovanni tries to explain, but Sird steps in and tells him that he shouldn't over exert himself. Sird offers to explain everything herself and tells Orm to bring Giovanni back in the ship. Red tries to stop Sird, but she and Orm send their Pokémon to surround Red and Yellow.
While Orm takes Giovanni away, Sird begins telling the story of Deoxys's birth. Red states that he already knows that Deoxys is a Pokémon from outer space that was mutated from a virus. Sird continues her story to when a rocket was fired into space by the Mossdeep Space Center. The rocket found and investigated the virus, which soon mutated into two life forms. They attached themselves to the Grand Meteor, where they fell to the Hoenn region and was found by Professor Cozmo. After a spy reported the findings to Team Rocket, they guessed that the life forms would become very powerful Pokémon.
When Hoenn was plagued by a catastrophe, the Space Center was attacked by the Magma Admin, Courtney. Although they were unsure of her motives, Sird used the opportunity to take the two life forms away. On the battleship, they monitored the life forms and found out that they had powerful psychic powers that allowed them to find objects from far away. When she showed them to Giovanni, Sird pointed out that they could be used to find his son.
Sird tasked Ken, Al, and Harry with taking the life forms to Kanto. Once the life forms were taken out of Hoenn, their appearances changed. They soon determined that depending on the area, the life forms could either change from their Normal and Speed Formes in Hoenn and the Attack and Defense Formes in Kanto. After learning more about the Formes, Sird came up with the idea to set up circumstances that would allow them both to switch between all four Formes at will. Later, Al reported the one of the life forms had escaped, much to Sird's annoyance at herself for trusting the three with the task.
Upon arriving at Kanto, Sird and Giovanni saw the destruction that the escaped life form had done. They soon found out that it went to Birth Island, where it set up camp. Giovanni assumes that the one called Organism No. 2 went to Birth Island so it can complete its shape and awaken itself. He notes that Birth Island is the perfect place for Deoxys to do such a thing.
Back in the present, Sird states that they allowed Deoxys to roam free to make its psychic powers stronger, but at the cost of making it harder to recapture. To rectify this, they used Organism No. 1 to attack Red and his friends to provoke and anger him. When Red asks what angering him has to do with anything, Sird states that Organism No. 2 reacts towards his anger. Remembering what Deoxys claimed earlier, Red realizes that Organism No. 2 is only drawn towards him.
Sird confirms this and states that besides herself and Giovanni, the other Team Rocket members were simply told that their target was all three Pallet Town Pokédex holders, when it was really just Red alone. She states that with the black Pokédex, they concocted a plan to capture Organism No. 2 after examining it during its battle with Red. When Yellow asks what happened to Organism No. 1, Sird states that they "disposed of it", as it was no longer useful. In her mind, Yellow expresses disgust at the fact that Team Rocket sacrificed one to make the other stronger, but notes that Sird is withholding the real reason why Deoxys claims that it is Red. Elsewhere, Silver awakens with his father lying down next to him.
- Organism No. 2 reveals that it believes that it and Red are the same.
- It is revealed that there are two Deoxys named Organism No. 1 and Organism No. 2.
- Sird explains the Deoxys's past.
- Silver awakens.