In the Star Trek Universe anything that is in a television episode or movie is considered Star Trek Canon. Anything that is written is considered non-canon but is excepted as long as it doesn't contradict the canon. The cartoon television shows are a little more controversial. They are generally excepted as canon but not by everyone or officially. It is because of this that the Media will be listed first on this page followed by the comic history.
The Doctor or Voyager: Emergency Medical Hologram Mark I was developed as a program to help should all the medical staff be injured, killed or missing, being unable to perform their duties. The program however was never intended for long term. He was programed with the ability to treat any aliment and know any medical history. He was created at Jupiter Station by Doctor Lewis Zimmerman, with the help of Reginald Barclay and he was also made in Zimmerman's image.
Please, state the nature of the medical emergency -- Voyager: Emergency Medical Hologram Mark I
On 48308.2 or 2371 Earth Calendar The Doctor was activated when Voyager entered the Delta Quadrant. The Doctor stayed on as the Medical Hologram because Voyager was so far from home and was unable to get back home for a replacement Medical Staff. As he stayed on Voyager he was given more rights as a sentient being. He became able to activate and deactivate his own program.
Eventually Kes would work with the Doctor as his assistant and she became an advocate for him to become more human and get more rights as a part of the Voyager crew. The Docter really liked Kes and developed a deep friendship with her and he even had romantic feeling for her but he was never able to pursue any relationship before she left. Kes also helped the Doctor become more human and sensitive to other people. She commented on his bedside manner and got him to give himself a cold. She extended the term of the cold to teach him a lesson on understanding his patients better.
The Doctor even started to go on away missions and went on other parts of the ship but is was extremely limited until he got his portable holo-matrix. That allowed him to move anywhere freely. The Doctor would also develop a supplement to his program as a Emergency Command Hologram.
Eventually, after three years his good friend Kes left and he missed her very much. He would make a new friendship with Seven of Nine. He also fell in love with her. Much more deeply than he had with anyone else but his own insecurities kept him from pursuing the relationship.
After seven years he and the Voyager crew would get back home. As far as canon stories is in not sure what happened to the Doctor. There have been other stories that were written about the characters but they were non-canon.
There were many stories written about voyager and several comic series mainly written by Marvel Comics.
In one instance, the Doctor's program becomes intertwined with the Holodeck recreation programs. The crew has to figure out where the problems lay; with the holodeck or the Doctor's internal systems.
In the one shot 'Mirrors and Smoke' we see the Doctor from the Mirror Universe. Here he is simply used as a tool to keep the crew healed. There is no consideration given to him past that point.
The mysterious new arrival Annika Hansen changes this. She treats the Doctor as a sentient entity, allowing him to become his own person. Who mutinies. With the help of Annika, the ship is overtaken; this includes the murder of several crew, including Commander Cavit.
Janeway repels the Doctor's mutiny by calling on the aide of the powerful pirates Neelix and Kes. In the chaos, the Doctor is rebooted back to his original form, obliterating the humanity and what little progress he had made over the years.