I guess what's unusual here is that we're used to seeing the character of Moriarty introduced at a point when Holmes is already aware of him and has been tracking him for some time -- but here we're coming in on the ground floor, seeing the moment when Holmes first became aware of a shadowy criminal mastermind.
Exactly. At this point, pretty much everything Holmes knows about Moriarity is a name on an index card, surrounded by a lot of empty space. As represented by that final scene.
Moriarity (whomever he or she is) has obviously been aware of Holmes for some time, but Holmes only just now became aware of Moriarity's existence.