Plan for Mulder in "Herrenvolk"

At the end of "Herrenvolk" (Season 4), as the Alien Bounty Hunter

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

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

and so Mulder might fit into the plans in that way.

However, it is not clear that this outcome could have been anticipated, as

So then, what is Mulder's importance to the plans for colonization?