By Roger Ford and Noah Snyder.
On the map, each puzzle is indicated by a college shield. (There's also one for the University.) Each corner of each shield is a nautical signal flag, which represents a letter. That gives a set of 2x2 letter squares. For example, the University of Cambridge shield gives:
Each column of each shield, save two, overlaps with the other column of a different shield. Thus the shields can be overlapped to spell out two lines of text:
Dana Scully is the third spy; she is hiding in Washington, DC.