EDIT: I forgot to mention that he had worked with the NYPD on behalf of the CIA as a counter-terrorism adviser from late 2001-2004. Then he want back to working with the CIA, but the NYPD asked if they could hire him onto staff and he stayed with the NYPD after that, retiring from the CIA in 2009.

I think people have been getting confused by the NYT's use of the word 'embedded' which implies he was working for the CIA while spending his days with the NYPD, much as a journalist files reports to his TV or print media employer while embedded with the military. It's an odd choice of words, as nothing in the report suggests that this was the case.

https://www.documentcloud.org/documents/717864-cia-nypd-ig.h...