Obviously, if John Doggett committed some horrendous crime against humanity or betrayal of Mulder and Scully and Skinner in the final season of X-Files I'm unable to comment. From the perspective of most of season eight, the characterization of John Doggett is beyond this reproach. When he first appears on the scene it seems certain that Special Agent John Doggett is a career oriented jerk who could be the Director of the FBI some day, and yet it is obvious early on that Doggett, like renegade agents Mulder and Scully, does have truth and human good as his goal.
Special Agent John Doggett has experienced great success at the FBI after a fruitful career as a police officer. Whereas Mulder and Scully have been marginalized and mocked in the Bureau, neither of them capable of having a normal outside of their work, John Doggett had a wife and a child. He's one of the guys when he's at work, able to engage in manly water cooler talk. He laughs and mingles and it seems like he has the life that Mulder and Scully can never have. But this is just a superficial view of a deeper sense of brotherhood and camaraderie which, combined with his devotion to always doing good police work, makes him perfect for the X-Files. It is clear that the duty to ones partner, whoever that may be and whatever she may believe, is central to John Doggett's characterization. In this case, his partner is Dana Scully, and his duty to partner resembles a kind of love. Doggett hunts for Mulder with great vigor because it matters to Scully. He pushes himself to be a good cop while on the case, but he also pushes himself to do the difficult job of entertaining the impossible, and this comes from respect for Scully. He is seriously disturbed by Scully's absence and evidence of hospitalization, and this is because he truly cares for his partner.

In the face of such a shining character, how can people justify this negative attitude toward John Doggett? The answer is simple. John Doggett is cool, but he's no Fox Mulder. I completely agree. John Doggett is not Fox Mulder. He's a completely different character, incomparable to Fox Mulder, never intended to be or become Fox Mulder. John Doggett is his own man. If John Doggett were judged by his commitment to the X-Files, to Mulder and Scully, to the truth and to the United States of America, to being a really cool dude that we enjoy on screen, he would be one of the most glorified names in modern sci fi. Unfortunately, he's judged only by the fact that he replaced Fox Mulder as Dana Scully's partner. John Doggett is denied a personal identity. For all intents and purposes we might be better off calling him not-Mulder, because that's what we've reduced him to.

But that is not the ending we got. We lost David Duchovny/Fox Mulder before the story could be properly concluded. As a band-aid, Robert Patrick/John Doggett was introduced to lead us to the end. He was the best band-aid we could have gotten. I propose that we stop making Special Agent John Doggett our scapegoat for the possible shortcomings of FOX, Christ Carter and David Duchovny. All I am saying is give John Doggett a chance.