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Sophia (ソフィア, Sofia) is the strange dark goddess who appears in .hack//Quantum. She kills those who come to the dark tree, and her victims become Lost Ones. Very little is known about her, though Shamrock knows more than she is willing to tell.
The dark Sophia in the OVA, based on information in the .hack movie, is likely a virus-infected anti-virus program which normally would have protected against the virus being unleased, but instead infected players and put them in comas.
.hack//Beyond the World
An updated version of Sophia appears in the .hack movie. It appears that they are actually anti-virus programs sold commercially by CC Corp, which may explain why Reiko Saeki knows about them, having possibly been involved in their development. The World contains many Sophias which arrive in areas being attacked by viruses and glitches. They are controlled by a main Sophia called Auto Sophia who performs something akin to a Data Drain on viruses.
It is later revealed that CC Corp was able to replicate Aura's Data Drain abilities, and created the Sophia programs with these abilities in order to be mass-produced as anti-virus software. Furthermore, the mutating Virus Bug was shown to have also been released undercover by CC Corp in order to promote this new product. However, the virus proved to evolve too fast for the Sophia programs to subdue, and it soon began to hunt them instead.
Kite(Sora) witnessed a group of Sophias be absorbed by the Virus Bug before it was Data Drained by the Auto Sophia. Unfortunately, the data of the engulfed Sophia programs was incorporated into the virus data during Data Drain's rewriting process, evolving it into an all-powerful virus which emerged from the Drain and devoured Auto Sophia.