I think it's clearly the plants. The original script, as some have pointed out, was titled "The Green Effect" (and I believe an even earlier draft was titled "Green Planet"). The film goes out of its way to focus on the plants, and show a specific cause-and-effect relating to the plant theories. It shows us multiple experts within the film talking about it with certainty, too.

Not only that, but the film goes out of its way to show us a nuclear power plant behind the house of the couple that owns the plant garden. Someone mentions that there are lots of nuclear power plants in the Northeast, which is where the event is confined to, as well.

To cap it all off, the ending takes place in France, which is known for procuring most of its national energy from nuclear power.

So, the film may stop short of stating things outright, largely because Night doesn't like to do that sort of thing...but it's pretty clear that it's a) coming from the plants and b) spurred by the existence of nuclear power.