Through a Glass, Darkly is a novel where two Delta Green agents investigate a supposedly-dead boy, who shows up years later in perfect health. From Arc Dream's website:

"Born of the U.S. government's 1928 raid on the degenerate coastal town of Innsmouth, Massachusetts, the covert agency known as Delta Green spent four decades opposing the forces of darkness with honor, but without glory. Stripped of sanction after a disastrous 1969 operation in Cambodia, Delta Green's leaders made a secret pact: to continue their work without authority, without support, and without fear. Delta Green agents slip through the system, manipulating the federal bureaucracy while pushing the darkness back for another day—but often at a shattering personal cost."

Ten years ago, everything changed. It's time you found out how.

It's January 2001. The Delta Green agents code-named Cyrus and Charlie get the call: A young boy dead and buried for years has reappeared, healthy and happy, as if no time at all had passed and the disease that killed him had never been. The family thinks it's a miracle, but Delta Green has seen too many miracles turn to madness. Cyrus and Charlie must discover what horrors lurk behind this one. The mission brings them to the brink of apocalypse -- to the edge of the revelation and destruction of Delta Green -- to secrets and terrors at the heart of reality itself.