The Virus Program was a computer virus created by Dorothy's creators, Albert Steiner and Dr. Pascalle, and was written onto the brain of Lilia Pascalle. In the event that Dorothy would disobey her human creators, the two scientists wrote a program that would infect her systems and destroy her. While Dorothy was a super-computer and had control over Michelangelo City, she lived in fear of the virus program. She sought out the destruction of it and used her Galerians to accomplish this during the events of Galerians and it's movie adaptation Galerians: Rion.
Before the first game's events, Lilia had the program written onto her brain when she was young. This resulted in the manifestation of her telepathic psychic abilities that she uses to communicate with Rion Steiner. Like with Lilia, Rion had a different program written onto his brain when he was young. This Activation Program was needed to use the Virus Program in Lilia's mind to destroy Dorothy as both of them by themselves were useless against the AI. While Lilia's surgery resulted in telepathic powers, Rion instead fell into a coma and was sick for a lengthy period of time. Sometime after this, Albert Steiner and Dr. Pascalle realized that Dorothy was aware of what they were doing, sending Rabbits and the Galerian, Rainheart, to spy on them. They decided that it was two dangerous for them to be together and Dr. Pascalle took his daughter away from the Steiner mansion and went into hiding. Lilia and Rion would not meet face-to-face again until their reunion at the Babylon Hotel.
Despite the actions of Dorothy's creators, they could not save themselves from her wrath. She eventually decided to kill them and she sent Rainheart and Rabbits to complete this task. Albert Steiner, his wife Elsa Steiner, and Dr. Pascalle were all murdered while Rion was captured and taken to the Michelangelo Memorial Hospital for experimentation, where he would later die and be replaced with his Galerian clone as a plot by Dorothy to find Lilia and the virus program. Lilia herself was fortunately on the run from Dorothy and was not present at the Steiner mansion during the time of their murders.
Rion, thinking he is the human Rion, eventually escaped the hospital and killed numerous followers of Dorothy, including Dr. Lem and three Galerians - Birdman, Rainheart, and Rita - who were hunting for Lilia, and reunited with Lilia at the Babylon Hotel. After breaking into the Mushroom Tower and killing his twin brother Cain, Rion met Dorothy and defeated her in battle. While dying and in shock of her creation's rebellion, Rion told Lilia to send him the virus program and using the activation program in his mind, he downloaded it into Dorothy's systems and completely destroyed her, even causing her physical body to explode and blow a hole in the top of the Mushroom Tower. While the two were successful in killing Dorothy, downloading the virus program and activating it caused his brain to crash and Rion died lying in Lilia's arms. He was then put into cryogenic storage by Lilia and was revived six years later during the events of Galerians: Ash. Unfortunately, Dorothy's backup program activated after her death and this resulted in Ash starting a war with humanity.
In the second game, Lilia told the recently revived Rion that the virus program was effective on the Last Galerians and their leader Ash. Despite Dorothy's efforts, she could not erase the weakness that was passed down to all her creations. Essentially, the program was a fail safe against not only Dorothy but also all the Galerians. Rion then decided to use the still downloaded virus program in his mind and use it to destroy Ash and free humanity for good. According to Nitro, she and the Last Galerians had thought that downloading the program into Rion's mind caused Lilia's telepathy to disappear but that was not the case, as Lilia sent the image of Cas dying in the real Airport Terminal to Rion who was trapped in Nitro's data world illusion. She also offered to Rion the chance to realize any wish he desired in the illusion world in exchange for allowing Nitro to delete the virus program in his mind, to which he refuses. Rion also appeared to use Lilia's program to destroy Nitro for good after their second battle.
At the end of the game, Rion battled with Ash in his Uranium Refinery and despite the Last Galerian's efforts, he lost in the end. Rion then told Ash that he was the virus program created to destroy Dorothy and all of her children, and that he was not called here by Lilia or anyone else, commenting that his intent to destroy the Last Galerians was something born from his own free will. Ash then meets his end after Rion downloads the virus program onto him, leaving them both suspended in the data world until Rion met Pat ten years later. Rion was told by Pat that the world was a better place because of Dorothy and the Galerians being destroyed but also that Lilia had died from radiation poisoning she suffered at the Uranium Refinery. He chose to have his and Ash's data deleted by Pat and this marked not only the end of the Galerians, but also the destruction of the virus program created to eliminate Dorothy.