It's interesting that along with the greatest complication of the x-files series (the disappearance of Mulder) we bring a major plot complication back into the story (the alien bounty hunter). The uncertainty evoked by the ABH in the characters that unknowingly interact with him in the story is indicative of the uncertainty fans begin to feel as the chances of finding Mulder grow even slimmer. "Within" describes Scully's search for Mulder in hear life and in her heart. Doggett's first appearance on the show attempts to undermine what Scully knew of her relationship with Mulder. She only questions herself for a moment and then refuses to play along with Doggett's game. This is a good first interaction between the two because Doggett is a old-fashioned copy who might rely on manipulation a bit more than Mulder and Scully usually do. She sees through this fairly quickly, which helps the respect begin to form between her and Doggett.
Scully's own personal feelings boil out but only in the privacy of her apartment while trying to call her mother and in Mulder's apartment when we truly see how much Mulder meant to her. The investigation may have a couple of plot contrivances, namely Kersh slipping Doggett Gibson's file, but overall, Doggett conducts the search according to what he knows of how to recover missing persons with only a half-hearted consideration of Skinner's pleas to consider an alternative theory OR Kersh's pleas to ensure that the FBI comes out looking competent and clean. Mulder's illness seems to fit perfectly with CSM's decline in health from "Closure" through "En Ami" and "Requiem." Perhaps Mulder's younger immune system was helping him fight the disease better than CSM's. But he was dying nonetheless. To an extent, this explains his willingness and readiness to accept his sister's fate in "Closure" and to open himself more to Scully in "Theef" "En Ami" "Je Souhaite" and "Requiem/." His tombstone does seem to be a little much and a little premature. But my thought is he just wanted to save Scully the burden of taking care of those funeral type tasks. Kersh's promotion almost seems to hit Skinner at just the wrong time. In "Paper Clip," Skinner wrote off the Syndicate route to power. In "The End" he provided Mulder a platform for his theories and his case against the government. So by Requiem, he had all but ruined his chances for advancement that seemed so promising in "Little Green Men" and even by "Tunguska" not totally gone. But once he accepts Mulder's beliefs as his own, he really does what Scully said and gives them the chance to ruin his career. Kersh is where Skinner could have been and Skinner recognizes this. But Skinner is beginning to accept his new role in things and how much of an ally he can be to Scully. His first task will be to win Doggett over to their side.