I think you mean antagonists. Protagonists are the heroes.
<evil grin>
Really?
Who's the protagonist in Die Hard? I'll give you a clue- it's not Bruce Willis as John McClane....
The protagonist is the person who's pro-active, trying to do something that drives the plot. Usually that's the hero (trying to find the Grail, catch the robber, win the war, etc) but not always. The antagonist is the person trying to stop him, or at least act in a manner that will get in the way of the protagonist succeeding.
So, in Die Hard, Hans is the protagonist, trying to rob $600million from Nakatomi, and McClane is the antagonist, trying to foil the plan which he has stumbled upon by complete chance.
It'd certainly be possible to have the Borg as protagonists - arguably First Contact counts, as it's the Queen's plan that drives the story.