Prior to the start of the chapter, Organism No. 1 and its twin, Organism No. 2, were created from exposure to strange radiation when they were viruses floating in space. After being mutated, they attached themselves to a meteor, which crashed into the Hoenn region and was found by Professor Cozmo, who took it to the Mossdeep Space Center for study. However, during Courtney's attack on the Space Center, Team Rocket was able to steal the two DNA Pokémon in the confusion.
Organism No. 1 first appears in Return to Pallet Town, attacking Red and Blue in Pallet Town. In Now You See Me..., Organism No. 1 appears as an invisible enemy on the Seagallop Ferry in which it attacked Green and easily defeated her Pokémon. It then kidnapped her parents by sucking them into a miniature black hole, causing Green to go into a coma from the shock of losing the parents she had wanted to meet for so long.
In It's Starting to Make Sense Now, it was revealed later that Organism No. 1 was used to provoke Red, whose anger would alert Organism No. 2, who was connected to him, and lure it so it could be captured. As Sird explained Organism No. 2's history, she mentioned that as they no longer had use for Organism No. 1, they "disposed of it".
Years later, Organism No. 1's fate was finally revealed. After the Grand Meteor Delta had been destroyed, a Deoxys emerged from its DeltaShield (Japanese: 三角形防御壁(デルタシールド)Delta Shield) inside the meteor and attacked Ruby and Sapphire, who had ridden Rayquaza into space in order to destroy the meteoroid. Down in Sootopolis City, Giovanni confirmed that this Deoxys was Organism No. 1, which Team Rocket had disposed of after it had served its purpose. Organism No. 1 was subsequently attacked by Rayquaza, destroying its core. As a result, the DNA Pokémon was left floating back into the depths of space where it had come from.
Prior to the start of the chapter, Organism No. 2 and its twin, Organism No. 1, were created from exposure to strange radiation when they were viruses floating in space. After being mutated, they attached themselves to a meteor, which crashed into the Hoenn region and was found by Professor Cozmo, who took it to the Mossdeep Space Center for study. However, during Courtney's attack on the Space Center, Team Rocket was able to steal the two DNA Pokémon in the confusion.
Organism No. 2 eventually broke free from captivity and escaped from Team Rocket. In the process, it accidentally absorbed a sample of Red's blood, causing a connection to form between them and leading him to believe that he was its ancestor.
On Five Island, the KantoPokédex holders are used to bait the Deoxys out of hiding. In Don't Doubt Deoxys, after confronting Carr, Red battles with the mysterious creature, starting the fight with Pika, attacking Organism No. 2 with a Thunderbolt. Organism No. 2 switches to Defense Forme and easily blocks the attack. Organism No. 2 then switches to Attack Forme and tries to tie up Red with its tentacles, while the other one turns into a fist. Organism No. 2 then sends a powerful punch at Aero's face, and follows the attack by piercing Aero's wings with its tentacles. Red then has Saur catch the falling Fossil Pokémon with one of his vines. Red sends out Snor, who attacks Organism No. 2 with a powerful punch. Organism No. 2 switches back into its Defense Forme, making the attack useless.
Red then sends out Gyara to battle, making notes how the forme with tentacles has a higher attack, while the bulkier forme has a higher defense. Pika fires off a Thunder attack at Organism No. 2's chest, hitting its core and dealing a lot of damage. Organism No. 2 quickly heals itself with Recover, and uses its PressureAbility to prevent the move from being used again. Organism No. 2 finishes the battle with a powerful Psycho Boost, defeating all of Red's Pokémon and causing them severe damage.
After the battle, Sird gives Organism No. 2 the Ruby and Sapphire, allowing it to unlock all of its formes. Organism No. 2 proceeds to transform into its Speed Forme and flies to Birth Island to recuperate its injuries from the battle.
In Going Green, Organism No. 2 creates its DeltaShield (Japanese: 三角形防御壁(デルタシールド)Delta Shield) to help protect it while recovering. This is cut short by the arrival of Giovanni, who came to the island in order to capture the DNA Pokémon. Giovanni sends out his Aggron to attack Organism No. 2, claiming that the power of outer space belongs to him. Organism No. 2 manages to get out of the way with Teleport. Although he praises Organism No. 2's skills and notes how the Delta Shield will protect it from attacks while also healing it, Giovanni states he can read Organism No. 2 like an open book. He sends out his Beedrill and has it use Agility so it can outspeed Organism No. 2. Organism No. 2 dodges Beedrill's attacks, but Aggron manages to smash the Delta Shield with a Brick Break. Giovanni then throws a Poké Ball at Organism No. 2, successfully capturing it.
In Secrets from Sneasel, Giovanni has Organism No. 2 uses its psychic powers to find his long-lost son. Organism No. 2 locates him and informs Giovanni that his son is in Viridian City.
Organism No. 2 and Giovanni
In Can Mewtwo Dish It Out with a Spoon?, Organism No. 2 is used to battle against Red on the Team Rocket airship, who had joined forces with Mewtwo. Mewtwo introduces itself to Organism No. 2 while the DNA Pokémon remains silent. Mewtwo then starts the battle, attacking Organism No. 2 with its spoon. Organism No. 2 easily maintains an advantage over the Genetic Pokémon, using its forme changes to counter all of their strategies. Due to this Red tells Mewtwo to just attack the crystal in Organism No. 2's chest. Mewtwo attempts to pierce the core with its spoon, but Organism No. 2 blocks the attack with its arms. Mewtwo then rushes into an attack, while Organism No. 2 rushes past it with its Speed Forme. As Organism No. 2 grabs Mewtwo with its tentacles, Mewtwo attack shoots an attack down and pierces the DNA Pokémon through the chest. Organism No. 2 struggles to control its formes and Mewtwo goes for the final blow. Organism No. 2 then stabs Mewtwo from behind with its tentacles, using an aurora to make it appear to be in its Normal Forme, when it was really in its Attack Forme. Organism No. 2 then uses Recover and prepares to finish the battle with Psycho Boost. Despite the power of the attack, Mewtwo continues to stand.
Red then rushes towards Giovanni and manages to steal the airship's remote controller and uses it to fire a barrier around Mewtwo. Organism No. 2 attempts to stop Red by grabbing him, but the energy manages to surround Mewtwo in time. Red tells Mewtwo to heal itself with Recover while he holds the DNA Pokémon off. Organism No. 2 then attempts to use its aurora ability, but Red tells Mewtwo that it's still in its Attack Forme. Giovanni tries to counter by having Organism No. 2 take Red into the sky with its Speed Forme. Since Organism No. 2 is moving too fast, Giovanni notes that Mewtwo might hit Red if it tries to attack. Red states that it doesn't matter and tells Mewtwo to attack Organism No. 2's core even if he has to hit him. Organism No. 2 changes into its Defense Forme and Mewtwo fires a powerful blast straight at its chest. The attack defeats Organism No. 2 and causes it to fall onto the battlefield below. Giovanni questions why Organism No. 2 turned into its Defense Forme when it could have easily blocked the move with its speed. Giovanni quickly notices that Organism No. 2 is rapidly shifting between its Attack and Defense Formes and he realizes that Organism No. 2 isn't in agony simply because of being hit by Mewtwo's attack, but because it can only shift between two Formes.
After the battle, Yellow arrives on the airship, and her powers allow her to hear Organism No. 2's thoughts while its origins are explained by Sird. When Carr hijacks the airship, Red helps the weakened Organism No. 2 and asks it to use its power to create black holes and send Silver, Giovanni, Yellow, and Mewtwo to safety.
After the four are sent to safety, Organism No. 2 helps Red to locate the explodingForretress hidden by Carr to blow up the airship. They dispatch all ten with ease and land the airship safely, and Organism No. 2 thanks Red and sets off to find its comrade, Organism No. 1, and find a region with special meteors that allow them to freely change between form. When it leaves, Sird is revealed to be alive after being thrown off the airship, and attempts to capture it. Red, with Yellow in his arms, Blue, Green, Silver, and Mewtwo jump in the way of Sird's attack to protect it, and all of them, except Mewtwo, are turned to stone as a result.