Manhattan will have an element of closure in Season 2, exec producer Sam Shaw has confirmed.
WGN has yet to confirm a third season of the nuclear period drama, but the show will resolve its key espionage mystery just in case the show is forced to end after Season 2, per Assignment X:
Yes, absolutely. That was the thing that was exciting to us. We spent the whole season last season writing about the human cost of a very destructive witch hunt for imaginary spies. There were a lot of people who were painted with the brush of espionage, and characters who were called traitors who weren’t, and there was a lot of human wreckage. By the end of the season, we finally reveal that one of our characters is a legitimate spy, and so this season, we tell his story, although I hope that we succeeded in telling the story in a way that will upend some of the conventions of spy stories. The truth is, there were real spies at Los Alamos, and their motives were really fascinating and complicated.