The burnt man is burned for a reason. In the opening scenes of Miracle Man, a younger version of the episode's "monster," Samuel, commands a badly burned corpse to "rise up and heal." The body rises but never heals.
Ten years later, the now-grown Samuel, working as an evangelical faith healer for a ministry run by his adoptive father, supposedly left a follower dead after "healing" her. Mulder and Scully come down to Tennessee to investigate and encounter the burnt man, Leonard Vance, now working closely with Samuel and his father.
When M and S find Samuel, Mulder begins seeing visions of his sister, Samantha, as a little girl dressed in an eye-catching red dress (nice touch from director Michael Lange). Interestingly enough, this is the one of the only supernatural things that the agents actually witness on this case. Most everything we see is revealed to be a trick: the locusts in the courtroom, the proof that cyanide killed the woman in the wheelchair, etc.
Samantha is always the symbol of Mulder's lost childhood - when his sister was abducted, everything went to crap for him, his parents got even more distant and then eventually divorced, etc. The little boy, happy go lucky version of Fox died when Samantha disappeared. That she's specifically wearing red in this scene suggests the ultimate coming of age we see in the Christ-like story of Samuel. Even though the child dies, that which comes after for Samuel and Mulder both will be improved.
Speaking of dying - despite Samuel's innocence, the local sheriff allows two of his men to beat Samuel to death in a jail cell. In another bold directing move, Michael Lange shoots this sequence in near silhouette, with Samuel adopting a cruciform position, mirroring Christ's penchant for taking the blame.
Samuel has to die because he comes to understand he's been laboring under a delusion. His father(s) lied to him, lead him astray, bought expensive jewelry with the money from poor, desperate people. Samuel is meant to remember that money is nothing compared to the sublime and he needs to be humbled.
He comes through the fire and is alive, and now must confront his bad fathers. Vance the burnt man blames his bitterness at having been resurrected into a scarred body. This is misguided because the life you receive, whatever form it takes, is always enough. It has to be.
The life Samuel received a second time seems to be real enough - as M and S get ready to leave Tennessee, they receive word that Samuel's body is missing from the morgue and witnesses have seen him walking around. Meanwhile, Sheriff Pontius Pilate is arrested in connection with Samuel's death. As Mulder and Scully leave, Mulder sees one last vision of his sister in red - a reminder that death is not an end, but a means to undergo transformation. Mulder should seek to heal the pain of his sister, die to his sadness for her, so that he can be reborn, harder better faster stronger.
Also of note, Miracle Man was the first episode of The X-Files written by Howard Gordon without his long-term collaborator Alex Gansa. Chris Carter helped Gordon flesh out the details of the episode.