Why he joined Salamandra will always remain a mystery. Still more mysterious is why he would choose to be number two. If it was willingly or because of blackmail, no one can tell. But he apparently was not very happy with his choice, he and Azar Javed having had certain differences of opinion. This is not to suggest that he was not perfectly happy killing innocent bystanders and just plain anyone he felt like. He seemed to have issues with the power arrangements.
When Geralt finds himself unexpectedly incarcerated at the beginning of Chapter II, it turns out that the Professor is one of his fellow inmates, but not for long. The Professor is bailed out of jail by persons unknown, leaving Geralt to stew, but not before taunting him a little, as bad guys do. Their second encounter comes at the end of Chapter II when the witcher must again face him and Azar Javed. Their third encounter is their last. It is the Professor's second last encounter with anyone or anything. His last rendezvous is with a hungry kikimore queen.
The Witcher 2: Assassin of Kings
The Witcher 3: Wild Hunt