I came up with one idea that was going to be used in the Sol Contingency game... don't know if it still is, I've been left out of the loop there for a while now.
It was quite clever -- didn't entirely match up with the previous continuity but that's what reboots are for. I'll expound when I'm positive I won't be spoiling anything.
One other idea I had was that it was a disembodied alien intelligence trying to figure out how corporeal life works by observing humans through their machines (sending parts of itself to Sol as nanotech to subvert those machines to its purpose), and isn't so much actively trying to destroy humans as just... not having a very gentle touch when it pokes and prods. It doesn't much care if it hurts someone, or if it wipes out a civilisation or three.
It used Tycho Brahe, the Mercenary planetoid, and four other planetoid-like objects as "listening posts" on this solar system and others, but after Dravis tried to subvert the virus and found out what it really was he was terrified of it; and even after gaining control over a portion of it he still had at least three of its planetoids (Tycho Brahe, the bees one, and Charon, and possibly one other), either destroyed or rendered unusable before his death.
Two of the other three were undiscovered by anyone on Earth at the point when the main games took place, and nobody but Dravis had any idea that the last one was anomalous at all.
This was a backstory for another big solo project I started and never finished, which picked up where Mercenary left off and went on till sometime after the ending of Descent 3.
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Much like the other one, I had it very well thought out. An interesting villain makes an interesting story after all.