Again, the government is up to no good, covering up evidence as soon as it arrives, incinerating all infected bodies. However, the motives of the government seems to be based on reason rather than an insidious plot of some kind. Containment of information--in this case, through the use of fire--may be helpful. By maintaining control of the situation by tracking those infected while keeping the public calm, the government is able to minimize losses.
So is the truth the best option in this situation? Mulder, who is prepared to let everyone know, never gets the chance to cross the line of revealing the truth to the public. Instead the government takes out the prisoner before he can speak. Effectively, Pink Pharmaceuticals used prisoners as lab rats without repercussions as the government either enable it for a short while or hid the facts.
Looking back at the episode, CSM's appearance makes no sense. At that time, he was just the face of whatever covert activity the government was conducting, but as his role was defined, he became the face of the Syndicate. Since there's no evidence of aliens, "F. Emasculata" is not a mythology episode.
Just a side note, Janet Reno look hideous. I mean damn... Well, at least her appearance sums up how gross the episodes is. Skinner has to replace that picture.
Score: 9.2/10
