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He had no control over his activation subroutines, so anyone could activate or deactivate his program solely at their choice.
Most of the crew considered him merely a computer program or a tool, and treated him accordingly.
As no one but he could be trusted, given that the Komar could inhabit anyone at any time, Janeway transferred her command codes to The Doctor so that he could countermand orders he believed were initiated due to the alien's influence.
Kes brought the matter to Captain Janeway's attention, asking that The Doctor be treated with greater respect and granted some interpersonal autonomy.
He, in turn, was curt and rude to them, lacking empathy and bedside manner, and he was unhappy that he was being used to perform menial medical tasks.
He felt that his perfection and comparative medical genius were not appreciated.
The Doctor quickly established that the Voyager crew would be stuck with him for a while and that he would be the sole provider of medical care aboard the ship.
( The Doctor's first few weeks as a full-time medic on Voyager were not easy for him.