A lot of good responses to this thread so far, but nothing that really fits yet. Perhaps some more information would help:
After being mind-wiped, the doctor began working for the cult out of a sense of gratitude (after all, they "took him in" after he woke up with no memories). The cult is directly guiding this work, giving him specific things to research in the hopes that they will be able to take his work and turn it to their own ends. They might corrupt it, or use it in a way that the doctor did not intend. It's important to note that the doctor does not know the true purposes of the cult -- he believes that they are a charitable organization.
I can easily see him creating something alchemical -- a serum, powder, poultice, extract, etc. I've thought of stuff that could heal/strengthen bones, keep a person alive after great blood loss (perfect for torture), put someone into a extremely deep sleep (the doctor thinks "surgery", the cult thinks "kidnapping"), etc. But even if these were turned to evil purposes, none of them seem serious enough to be considered a dire threat. I'm hoping that the raw creativity of the folk here can help me get over this block.