Exorcists and Noah;
DOLLs infected with and taken over by the Innocence virus become Exorcists. DOLLs infected with and taken over by the Dark Matter virus become Noah. The viruses seem to be utterly random, and attempts to force them to pick certain DOLLs have failed. When the virus infects but doesn't take over, the DOLL either becomes a Fallen or an Akuma, but both are very destructive and dangerous to anyone nearby.
The Story;
All over the world, DOLLs began to be infected with a strange virus that would cause them to go against precautionary programming and attack their owners.
No matter the firewalls or stage of decay, the virus was running rampant. However there seemed to a few DOLLs that somehow had the ability to follow the virus and stop the so called "Akuma" before things got out of hand.
The Black Order came about to study and attempt to create more of these "Exorcist" DOLLs that could fight the Akuma. However the strange glitch caused by a virus called INNOCENCE.EXE could not be replicated simply by infecting other DOLLs with the virus. Misinfected DOLLs simply became the Fallen and would attack anything around them just like Akuma.
The Order created tracking programs to follow the Innocence virus and find the DOLLs that would become Exorcists. This usually involved buying them from their previous owners, or just claiming them universal security risks and simply taking the DOLL. Some owners follows their DOLLs to the Order, but it was not a welcome thing.
It was a fragile process, trying to customize the Exorcist DOLLs with weapons to fight the Akuma without destroying the delicate balance that kept their programming in harmony with the Innocence virus.
Meanwhile, a strange machine who called himself the Millennium Earl, began to collect Akuma around him, finding the few DOLLs who gained the same fragile balance with the Dark Matter virus as the Exorcists had with the Innocence virus. The Earl called these DOLLs his Noah.
The Noah had strange powers and could control the Akuma, causing nothing but destruction in their wake.
And so began the war between the Noah and Exorcists.
Meta Info;
Although it's being studied the scientists haven't found any of this out quite yet. the Innocence and Dark Matter virus actually has a alternate effect of giving the DOLLs the options to decide which of their command functions to follow--basically giving them the option of freewill.
It also unlocks their emotional programs and gives those the ability to also override other programs--allowing the DOLLs to become irrational and overwhelmed with emotions.
tl;dr, the viruses actually make them more human, but no one knows this yet.