"The Long Journey Home" by Cary Bates, Greg Weisman, Rafael Kayanan, and Romeo Tanghal.
Having never read the Captain Atom title, I'm not exactly sure what the lead up to this is, but it seems as though the good captain has died!
And of course, when you visit the other side, The Phantom Stranger is there to meet you:
...he shows up at the end of the issue, too, (along with Death and The Black Racer!), to inform Captain Atom he has to take on Nekron, Lord of the Unliving! Gee, thanks Stranger!