Author's Note
It took me a moment to work out how to answer Catspaw's question - it's been so long since I wrote this and quite some time since I last read it that I honestly couldn't remember for a moment. In short, the Vulcans' who originally gave them the nanobots were Shades', as I call them - the same race as the Dark Man. But they were of a faction that honestly wanted to make contact with the real Vulcans at Titrinus, where there was a Vulcan ship known to be currently in orbit. Let's call them the Good Guys. The Dark Man was of the opposite faction, the Bad Guys - he didn't want his race to make contact. He used Malcolm as the perfect way to saboutage the Enterprise's journey, ensuring the nanobots belonging to the Good Guys wouldn't get there. As the Good Guys had essentially helped the crew, they felt it their obligation to deliver the nanobots to the Vulcans as promised.
I think.
Thanks for reading!