The Borg war is at its height when the Enterprise is overtaken and hailed by a really small (approximately grapefruit-sized) spaceship at Warp Nine. It turns out to be the Nanite equivalent of a REALLY big spaceship, say a superdreadnought / Borg Cube sort of thing, and they're looking for God, and want him NOW. So where is Wesley Crusher when you need him?
Fortunately the Enterprise is still talking to them (from the Nanite point of view negotiations have taken a good few generations, but they're not too bothered since they're letting their computers do the work - owing to an odd software glitch the computers come across as California surfers, "yo dudes!") when the Borg turn up and start attacking. At which point Picard and the Borg learn that size isn't everything, as the Nanite ship launches a few trillion nanomissiles, which start taking the cube apart atom by atom and liberating the enslaved nanotechnology that make the Borg transformation work.
Not sure where it goes from there, except that the Nanites eventually turn out to be even more of a threat than the Borg - the Federation uses a lot of nanotechnology, one way and another, and they want to liberate it all. But of course Picard somehow rises to the occasion.
Someone really ought to write it, but it sure as hell won't be me. Now I'm trying to figure out what the hell gave me this idea, why I think surfer dude nanites are cool, and why I can't get my imagination to work like this when it's actually needed.