Long before Torchwood, Earth bound Dr Who worked reasonably well with UNIT, the Brigadier, etc. Assignment: Earth, as mentioned above, is an already established part of Trek and would be the obvious starting point if set in the 2020's. Who is that species giving these agents their tech and are they known in the 23rd-24th Century? A lot of possibilities there. Alien tech/incursions, time travelers, Temporal Cold War, contemporary Government agencies, etc.
I do think a WW3, Col. Green, First Contact era setting has a lot of potential also, but that is not set "today". Thats decades from now.