It can be said without argument that without her medical knowledge their cases would have gravely suffered. Imagine the Pilot without the sight of Scully calmly telling Mulder the corpse of Ray Soames was an alien, "possible an orangutan." In the world where no one can be trusted, how reliable would a normal pathologist be? It is clear that Mulder also realizes the importance in having an autopsy-gifted partner. His panic at seeing a military pathologist perform Duane Barry's examination in "Ascension" proves this nicely.
A vital part of her character is her medical background. To Scully this is a proud accomplishment and something she cares deeply about. Every autopsy she performs is making a difference - and making a difference is exactly why she joined the FBI. By identifying a John Doe's cause of death, she is not only putting him to rest but also helping a case in a very important way. I feel that this is at the heart of her autopsies - she is not merely doing what Mulder asks her to, she is doing something that she cares deeply about and knows that she is good at. This opinion, that she is only doing them because Mulder orders her to do so, is completely ludicrous. First, she does not take orders from Mulder. She never has, and I have confidence that she never will. Secondly, as I have touched on earlier she is doing them because she wants to. Examine the look of need on her face as she states "Order an autopsy," to Detective Kresge in 'Christmas Carol.' Clearly this is a woman who believes what she is doing is right, and feels a need to help the victim by unraveling the mystery behind their death.
In 'Bad Blood' we see a Scully who is bored of everything, autopsies included. Clearly, this is exploited for comedy's sake but we must also assume this is a side of her. As for her boredom, this can also be used to point out her apparent interest in the cases behind her victims. Throughout the episode, it is made clear that the victim's were of no interest to her. The supposed vampire deaths were trivialized, therefore distancing them from her. Also, this is a Scully who just needs a good vacation. And who doesn't get burned out doing the same job day after day?
Agent Scully has performed autopsies across the country in countless hospitals, even in the Arctic. Each time she does, an X-File case gets a dash of science as well as some concrete answers. In doing so, she adds credibility to their work and investigations. Answers are scarce in their cases, and using her forensic background she is able to provide some. In the situations that she cannot, this is when she is most bothered. She takes it upon herself to get to the bottom of what happened and when science cannot explain it she needs something to fall back on. In this way, her autopsies are also vital to her attitudes about work. By performing them, she can convince herself she is doing all she can and that she is indeed making a difference.
Dealing with past demons of a personal nature, she has repeatedly used work to bring her out of it. As said best in 'Beyond the Sea' after her father's death, when a tearful Scully stated, "I love this job," her passion shone through. Her work includes her autopsies, and this is one reason why I firmly believe she is imperative to the X-Files. To truly excel at something in the level that she does, you have to have that love. She truly loves her work, autopsies included.
Scully in scrubs is truly a sight to behold. Her determination and seriousness are breathtaking, as well as her cool professionalism. Behind a face shield eyes of steely strength beam down at the job at hand, as scalpel in hand she begins the Y incision. This scene has been created many times, and each time it creates an immediate feel of her intelligence. Her intelligence is the most valuable thing about her as an agent, not to leave out bravery and honesty. This intelligence is the driving force behind their investigations, and through these autopsies she is only demonstrating once again how valuable she is.
Working on the X-Files cases, she has repeatedly gone beyond the call of duty. Does Mulder appreciate her forensic experience? Yes, judging by past acknowledgements. Is it fair to say that her knowledge has been taken advantage of? Possibly, but if she is willfully helping an investigation that she cares about it would not seem right to call it cruel. Well, except for that elephant in 'Fearful Symmetry.'