I was going to say sounds like The Happening!

I would make it about evolution occurring too fast for species to adapt.

How about a bird zombie concept? Massive numbers of birds die, drop from the sky, only to come back to life days later... zombified.

A doctor races to understand the infection before it spreads to humans...

Something like that.

From Wikipedia, bird deaths "most likely occurred because of some electromag­netic interferen­ce on a grand scale. Birds have, in their brains, an ability to detect the Earth's magnetism. They need to migrate. A significan­t electromag­netic disruption­, solar flare, EMP, maybe a bolt of lighting, can cause substantia­l disorienta­tion, brain damage at the very least causing the birds to fall out of the sky in a daze, dying on impact." http://en.wikipedia.org/wiki/Bird_migration

I'd probably run with that, electromagnetic cause, and only our hero figures out disturbance is not from natural causes, but rather symptom of nefarious activity.

@Evan - sounds like we could have a Birdemic on our hands.

http://www.youtube.com/watch?v=Yy-9YLpC5uM