My theory is satellite retrieval, Not ours, theirs. Play the long game, year two of a three year mission, do a little unannounced orbital dance, somebody's spy satellite has a unexpected failure, while really it is now in the rf shielded environment of the x-37's payload bay. Year three, bring it down for study.

Yeah, probably way to much science fiction there, way too many things would go wrong, and spy satellites tend to have huge antenna have fun trying to stuff that in a rather small payload bay. However... One of the space shuttle mission profiles was to deorbit a satellite. Officially, the space shuttle never did this. But I think the airforce really liked the idea and wanted to retain the capability.