(Capcom's primary storyline)
Stuart highly admired Wesker, referring to her as a scientific genius and believing she's the one who can create a perfect order in the world. Stuart's admiration to Alex led him to turn a blind eye to the pain and agony their test subjects experienced.
Stuart made some notes regarding Claire Redfield, Moira Burton and Natalia Korda during the Sushestovanie Incident. He also took note regarding Korda's status as Alex's chosen candidate above all other subjects.
As her loyal servant he did everything to help her achieve her goal, even at the cost of his own life. After his work was done, he made sure all researchers are dealt with (himself included), to ensure there are no distractions to the plan.
Further notes Edit
There is a hanged corpse right in the office where Stuart's last word was found. It is implied that the hanged man is Stuart.