If the runner is playing the virus deck, and trashes the top card of R&D, which happens to be an agenda, does the runner score it?

The runner would then need to run the corps Archives before scoring the Agenda.

Gaztingo is right.

And please note that Noise's ability trashes the card face down (at least, that is the way it is implemented in octgn).

Another thing that is sometimes overlooked: Crypsis has the keyword "Virus" as well, so its installation by a Noise player also causes a card to be trashed from R&D.

So the Corp doesn't get to see it either then, right?

The Corp can look at any facedown cards in Archives whenever they please. So they do get to see it.

I think that you don't score it. Because you have not Accessed it.

Page 18 of the rule book, Access Phase Archives. I think has the answer.

Happy Hunting

Rottencat