Oooh...methinks Kryptonite bullets are involved.
Surprising, though, that they'd have made them, having not done any previous tests to know that Kryptonite is harmful to Superman. I'm assuming that will be explained in the next part. And I'm wondering if Lois saw the first bullet bounce; she might be too distraught over the second bullet hitting Clark that she neglects to think about the first one.
Oh, and it totally makes sense that Bureau 39 would work in Area 51.