Remember - the Syndicate was formed around the time of Roswell, during the mid to late 1940's (I'm going from memory folks so feel free to jump in if I'm off course....). They were the human liaisons, between the human government and the aliens. The syndicate arranged things in secret, that they could not trust the gov't to handle, such as trying to create human-alien hybrids. So that had been why they were important initially. Once the aliens realized they were no longer needed for alien colonization to begin, the syndicate members were all eliminated (killed) toward the end of the series.
But - it's questions like these, that explain why we can fill enormous amounts of time trying to answer them.
The X-Files SEASON 10 * COMIC BOOK
Written by JOE HARRIS
** June 19, 2013 **