Comparing anything to Shield is a little difficult since I don't believe that the DCU has something comparable, there are too many different shadowy organizations. I wouldn't exactly call the Department of Extranormal Operations nefarious. They're not like Checkmate. The DEO's agenda is to monitor metahumans with extranormal abilities and safeguard the nation against any possible threat they may pose. Director Bones is their current eccentric leader...thus making them extremely enigmatic. We've been teased to their presence in prior arcs, I don't remember exactly when now...I think it might have been back in the Lois/Lana mini-arc when an agent of their was mention. I think it was Cameron Chase.
That is why I stated that it was genius of Q to have Bones offer Martha a position within the DEO given her previous stint as Red Queen of Checkmate. Q is not forgetting any of the show's continuity while tying everything together and further progressing the plots and character arcs. This is his true genius.