Assistant Director Walter S. Skinner of the F.B.I. is an ex-Marine.  At the beginning of the series 2 when he was first introduced to the X-Files he had very little patience with Agent Mulder's 'unorthodox' methods of investigation.  However, into series 3 he seemed to take notice of what Mulder and Scully are un-covering.  Once he shut down the X-Files entirely as he thought it was "entering into dangerous territory."  But when Agent Scully was kidnapped, he reopened them, telling Mulder, "That's what they fear the most".  I think it's obvious that 'they' are the government.  I often wonder whose side Skinner is on,  but his efforts for Mulder and Scully "through unofficial channels" have made it clear that he is deeply concerned about his special agents and their work.                                                             

I think that Skinner will be shown to be involved in a thickening plot very shortly . . .