Omega Ruby and Alpha Sapphire
In the Delta episode unlocked after completing the game, Deoxys travels to the Pokémon planet using a massive meteor, large enough to threat the planet with a mass extinction event. It is up to the player to summon Rayquaza to destroy the meteor and save the planet from destruction.
Super Smash Bros.
In Super Smash Bros. Brawl, Super Smash Bros. for Wii U and 3DS, and Super Smash Bros. Ultimate, Deoxys is a summon Pokémon that can come out of a Pokéball. When summoned, it will turn into its Attack form, fly upwards, and shoot a powerful Hyper Beam from its crystal core in a downward angle.
In Brawl and Smash Bros. 4, Deoxys appears as a trophy, both in its Attack Form. Also in Brawl, Deoxys appears as sticker, also based on its Attack Form, that grants additional damage to slash attacks for all Pokémon fighters. In Ultimate, Deoxys is a Grab-type Primary Spirit, and one of the few legendary spirits to have no support slots. When equipped, it increases Ness and Lucas' PSI powers. Its Spirit Battle is against Mewtwo that has increased attack power and summons Deoxys through a Pokéball.
The first one bore a purple crystal visible in its chest. It arrived at the North Pole four years before the events in the movie took place. It was in search of another Deoxys, which bore a green crystal in its chest. However, the purple one was attacked by a Rayquaza while trying to retrieve the meteor containing its friend. The purple one was defeated, and the meteor containing its friend was taken by Proffeser Lund for research.
During the four years that the first Deoxys was regenerating, Tory Lund befriended the energy form of the second Deoxys. Terrified of Pokémon, Tory did not realize that he had befriended one. However, at the same time Ash and his friends arrived, the first Deoxys was fully healed and headed to LaRousse City. There, it constantly released auroras to ask where its friend was, and since there was likely no reply, it multiplied itself to remove any living thing that caused an interference and any electrical device as they clouded its vision.
Later, with the help of Rebecca's computer, Ash and his friends worked together to reunite the two and regain the city's power. Yuko managed to extract the second Deoxys from the meteor with the help of Plusle, Minun and Pikachu. Much like the way Celebi carried Ash and Sam with its psychic power in Celebi: Voice of the Forest, Deoxys carried Ash and Tory with its psychic power, too.
Eventually, both Deoxys were reunited, but were attacked by Rayquaza once again. After Rayquaza was engulfed by the Block Bots and Tory fell trying to save Plusle and Minun, the second Deoxys saved him while the first one carried Ash and Pikachu with its psychic power. After a safe landing, they departed LaRousse City and returned to space.
Role in the mangas
Two Deoxys play major roles in the events of the FireRed & LeafGreen chapter, referred to as Organism No.1 and Organism No. 2. Organism No.1 returns in the Omega Ruby & Alpha Sapphire chapter as a villain.
Organism No. 1
A flashback revealed that it 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 space Pokémon in the confusion.
In the FireRed & LeafGreen chapter, Organism No. 1 first makes an appearance 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.
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".
In Omega Ruby & Alpha Sapphire chapter, Years later, Organism No. 1's fate was finally revealed. After the Grand Meteor Delta had been destroyed, a Deoxys emerged from it 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 died and was left floating back into the depths of space where it had come from.
Organism No. 2
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.
Organism No. 2 first makes its appearance on Three Island, where it saved Lostelle from a biker gang, though its intentions for doing so are unknown; its name is revealed here by Giovanni.
On Four Island, the Kanto Pokédex holders are used to bait the Deoxys out of hiding. After confronting Carr, Red battles with the mysterious creature, but is unable to win despite his best efforts. The battle left Organism No. 2 heavily injured, forcing it to retreat to Birth Island to recuperate inside of its Delta Shield (in Japanese: 三角形防御壁(デルタシールド, Delta Shield). This is cut short by the arrival of Giovanni, who came to the island in order to capture Deoxys. Deoxys attempts to avoid Giovanni's attacks, but Giovanni easily sees through its movements and breaks through the Delta Shield, leaving the exhausted Deoxys unable to escape capture.
On the Team Rocket airship, Giovanni uses Deoxys to battle Red, who joined forces with Mewtwo. After a long and tough battle, Red and Mewtwo emerge victorious. Yellow also arrives on the airship, and her powers allow her to hear Deoxys's thoughts while its origins are explained by Sird. When Carr hijacks the airship, Red helps the weakened Deoxys and asks it to use its power to create black holes and send Silver, Giovanni, Yellow, and Mewtwo to safety.
After the four is sent to safety, Organism No. 2 helps Red to locate exploding Forretress hidden by Carr to blow up the airship. They dispatch all ten with ease and land the airship safely, and Deoxys 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.
Pokémon Diamond and Pearl Adventure!
Deoxys plays a large part in a special chapter of volume 3 in the series. Harets and Mitsumi come upon a large meteorite in Veilstone City. Mitsumi proceeds to tell him that there is a Pokémon that comes from a meteorite. He tells her that he's met Deoxys. She freaks out and doesn't believe him, so he tells the story of how he met Deoxys. Hareta is seen jumping around the forest until he starts riding a Drifloon. A Murkrow flies toward them and pecks the Drifloon, causing it to explode.
Hareta is seen plummeting to the ground, and then bouncing off a Bibarell's stomach. He lays down on the ground with the Bibarel as a pillow, when the Bibarel starts getting worried, because it sees the meteorite containing Deoxys zooming to the ground. The Bibarel tries to tell Hareta what's happening, and he looks up and wonders what it is. The Pokémon and Hareta try to get away as the meteorite crashes down.
Deoxys emerges from the meteor, and Hareta thinks it might be a Pokémon. Meanwhile, Mars and some grunts see the crash, and begin to battle it, but to no avail. Proffesor Rowan shows up, a little worried that something might've happened to Hareta. He asks Rowan what happened to "that weird Pokémon". They then see Deoxys, and Rowan is shocked to see such a rare Pokémon. It transforms to Attack Forme and fires off a Psycho Boost at Hareta and Rowan. Rowan tells Hareta not to make it any angrier, but instead he jumps on top of Deoxys and asks what's wrong.
It flings him off, then tries to fire another Psycho Boost at him, but he jumps around it, evading it completely. He jumps on it again, but it transforms to Speed Forme while he is still on it. It starts flying around the forest with Hareta, while he asks Deoxys what's wrong once more. It tells him what's wrong, but it throws him off itself. Then he battles Deoxys with his friends from the forest. Onix tries to Headbutt it, but it misses. It transforms to Defense Forme, and then Hareta jumps on Deoxys and covers its eyes.
Then he tells a bunch of Kricketune to have a "super bug concert". Rowan compliments him on the super-effectiveness of the attack, then it transforms back to Normal Form. It becomes calmer, but transforms to Attack Form and fires off another Psycho Boost, this time hitting a Drifloon. It explodes, defeating Deoxys. Deoxys is totally calm now, and it merges its tentacles to create a hand, and it shakes hands with Hareta. Hareta finishes telling the story to Mitsumi, and tells her that it wanted to find out more about this planet.
- Deoxys' name is based on the first letters of "Deoxyribonucleic acid", or DNA.
- Deoxys is the 386th Pokémon in the National Pokédex.
- Deoxys appears to draw inspiration from certain representations of aliens and visual representations of the DNA double helix.
- Using the first letter from the names of three of Deoxys' forms, one can spell "DNA" (Defense, Normal, Attack). The letter "s" at the ending of Deoxys's name could stand for Speed.
- He seems to be Rayquaza's archnemesis, having confronted him twice.