Doctor Brundle was a scientist at Nezumi Testing laboratories. He was working on something that required animal testing.
According to the notes he left behind, his work relied extensively on testing things on living animals, specially rodents. When his colleague, Dr. Piccinini, showed him his "Pet Project", he wasn't sure what it was, and speculated it was some sort of elaborate, although inappropriate, prank.
Eventually, he was disillusioned with the work that was being done, and feared the research was turning into something dark, beyond the realm of science. He tried to quit while he could when he saw the results of the research.
After he was attacked by a crazed Dr. Piccinini, he tried to escape the facility using the flood tunnels connected to the rat fluid chamber, only to have his path blocked by Sotiris in the warehouse.
However, Dr. Brundle seemed to have successfully evaded Sotiris and escaped the testing labs- a newspaper laying on the street during the introduction was added in Version 2.0, stating that secret government tests had been revealed, and that "Dr. B" leaked the information to them with the inferred meaning that the information was given to the press by none other than Dr. Brundle.