The Structure of a Series: Holmes Omnibuses

After Holmes died, Doyle continued the series in two ways. First, some later written stories were set earlier, before the death. Secondly, other stories revealed that the death had been merely apparent. Thus, the series, in the order of publication, divides into three sections corresponding to three potential omnibus collections:

(I) two novels and two collections culminating in the death;
(II) two later written novels set before the death;
(II) three collections set after the return.

These sections are linked by the Moriarty organization:

(I) ends with the downfall of Moriarty;
(II) ends with Holmes planning the downfall of Moriarty whose chief of staff, we learn, is Sebastian Moran;
(III) begins with the arrest of Moran who had escaped after the downfall of Moriarty.

Thus, finally, the organization is destroyed. Other large, or at least important, organizations mentioned are:

the Scowrers, who engaged Moriarty to exact their revenge;
the Ku Klux Klan;
the Red-Headed League conspirators;
a German spy ring. 

However, the vast majority of Holmes' cases involve only local crimes or mysteries. Whereas James Bond later spent most of his time fighting either SMERSH or SPECTRE, Moriarty's organization appears only in the three works that link the three sections of the series.