At the end of "Herrenvolk" (Season 4), as the Alien Bounty Hunter
restores Mulder's mother at the behest of the Cigarette Smoking Man,
the Smoking Man explains to the Bounty Hunter in regards to Mulder that the fiercest enemy is the one with nothing to lose.
When the Bounty Hunter asks why he cannot simply dispose of Mulder, the Smoking Man insists that Mulder is an integral part of their plans — meaning the plans upon which the alliance between his Syndicate and the
alien colonists who once inhabited the Earth
is based. This leads to a natural question:
Which integral part of their plans was the Smoking man referring to, exactly?
Mulder, of course, is deeply opposed to the secret activities of the Syndicate. Much later, at the end of Season 6 and the start of Season 7 in the episodes "Biogenesis", "The Sixth Extinction", and "The Sixth Extinction Part II: Amor Fati", we find out that
Mulder has become a type of alien-human hybrid, one that required no surgical intervention or extended experimentation. His genetic code had been altered by a prior exposure to a form of Purity (most likely in Tunguska in the episode of the same name), and the result means that he is now the second truly successful hybrid, after Cassandra Spender. The creation of a slave race as part of the plans for colonization require successful hybrids,
and so Mulder might fit into the plans in that way.
However, it is not clear that this outcome could have been anticipated, as
Mulder's capture and exposure in Tunguska was not part of a pre-conceived plan, and the Smoking Man seems as surprised as anyone about Mulder's neurological condition and transformation in "The Sixth Extinction Part II".
So then, what is Mulder's importance to the plans for colonization?