So let's say that an alien civilization that we have made enemies with decides to use an advanced non-lethal biological weapon on the Earth as a warning.
The aliens, while not infamous for any technology, have unfathomable knowledge pertaining to chemistry and biology. Alien engineers create an organic crystalline compound (Organism X) that consumes atmospheric nitrogen N2 and duplicates its cells in an asexual fashion. It is fictitiously hive-minded, like the Necromorphs of Dead Space.
The catch: X's defense mechanism is to disperse nearby crystals into airborne microscopic clusters if LARGE numbers of cells are physically destroyed or disrupted. This includes burning, shattering, and collapsing if a certain crystal cannot support itself. These spread quickly, like a plague of sorts. After a time, the cells will consume enough nitrogen to fall to the ground again. They will starve if deprived from atmospheric nitrogen, including underwater and in a human's body. Cells in the center of a crystal receive nutrients from the outside, as long as they are adjacent to another cell.
Organism X enters Earth's atmosphere via a metal capsule that opens. Assuming it has dispersed due to the shock of reentry, it starts to spread quickly through, let's say, France.
How would a early-future society, say about 2040, eradicate Organism X? I imagine that time period to have technology similar to ours, with more VR, space travel, smarter AIs, much more efficient energy production, but not anywhere near an AI takeover. Like, Iron Man with Jarvis, not Ultron. So how would we kill off Organism X? Or does the "non-lethal" weapon turn into a metaphorical apocalypse that eventually wipes Europe off the face of the planet?
Edit: Perhaps it would be more appropriate to impede X's progress rather than obliterate it.