And let's remember that Agent Smith is itself attempting to take over the world.
In that case, it's presumed it was indeed a massive extinction (but no data to quantify any % over, due to no microbial fossils preserved).
... But for a different reason. It wasn't due to decrease in oxygen levels; contrary to that. At that time, oxygen was being first ever introduced into the atmosphere. This has left a unique geological trace we observe everywhere across the planet: the white sedimentary + red rust striped 2 Ga rocks.
The "microbes" were the first photosynthesisers. The oxygen was a toxic byproduct. Resistance to it had to be learned by evolution, and that learning took ~1e8 years. Many of life didn't manage to and went extinct.