In a flashback it was revealed that it and its twin Entity Two were created from an exposure to a strange radiation when they were just viruses floating in space, after being mutated they attached themselves to a meteor that crashed into the Hoenn Region where Professor Cozmo found it and took it to the Mossdeep Space Center for them to be studied. However During Courtney's attack on the Space Center Team Rocket took the two space Pokémon during the commotion.
Entity One 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 and in the process; it caused her to go into a coma from the shock of losing the parents she wanted to meet after so long.
It was revealed later that Entity One was used to Provoke Red so that his anger would cause Entity Two (who is connected to him) to seek him out so that they could capture it.
When Sird was explaining Entity Two's history she mentioned that after they no longer had any use for Entity One they "Trashed it", whether this means that Entity One is no longer alive or missing has yet to be revealed.
In a flashback it was revealed that it and its twin Entity One were created from an exposure to a strange radiation when they were just viruses floating in space, after being mutated they attached themselves to a meteor that crashed into the Hoenn Region where Professor Cozmo found it and took it to the Mossdeep Space Center for them to be studied. However During Courtney's attack on the Space Center Team Rocket took the two space Pokémon during the commotion.
Entity Two eventually broke free from its captivity and escaped Team Rocket's Grasp and in the process it absorbed Red's Blood into its body and gained a connection to him, eventually coming to believe that he was its ancestor.
Entity Two first makes an appearance on Three Island where it saved Lostelle from a biker gang (whether it’s intention was to save the girl or was just passing through is unknown), there we learn it’s name from Giovanni.
On Four Island the Kanto Dexholders are used to bait Deoxys out of hiding, after confronting Carr Red does battle with the mysterious creature, however he is soundly defeated and his spirit broken. The battle with Red however has left it hurt and exhuasted so it sets off to Birth Island to heal its wounds, however this is cut short when Giovanni arrives and captures it after a quick battle.
On the Team Rocket airship Giovanni uses Deoxys to battle Red who uses Mewtwo against it, after a long and tough battle Red and Mewtwo emerge victorious. After Arriving on the Team Rocket Airship Yellow’s powers allow her to hear its thoughts and its orgins are explained by Sird. After Carr hijacks the airship Red Helps the weakened Deoxys up and asks it to use its power to create black holes to send Silver, Giovanni, Yellow, and Mewtwo to safety.
After sending the four to safety it helps Red in Landing the airship by using its psychic powers to locate Carr's 10 hidden Forretress to prevent them from blowing up the airship with Selfdestruct. After the airship is safely landed it thanks red and sets off to find its comrade Entity One and find a Region that has a special meteor that allows it to freely change form, however when it leaves Sird (who is revealed to be alive after being thrown off the airship previously) attempts to capture it but Red, Blue, green, Silver, Mewtwo, and due to her being carried by Red Yellow jump in the way to protect it and all of them (minus Mewtwo) are turned to stone as a result.
