The NSA will adjudicate your application for a clearance after the polygraph, not before.

Regarding the consequences of refusal to submit to a polygraph interrogation, NSA's polygraph regulation (NSA/CSS Regulation 122-03) states:


Quote:

...refusal to consent to a polygraph examination, when it has been established as a requirement for selection or assignment to NSA, or as a condition of initial or continued access to classified cryptologic information may result in an adverse action, non-selection for assignment or employment, denial or revocation of access to classified cryptologic information, or termination of employment.  Refusal to take a polygraph examination shall be recorded only in the individual's security file maintained by the NSA Office of Security.  An individual's employer, shall not be informed of the refusal to take a polygraph, nor shall the personnel files be annotated, unless such refusal requires administrative action.

I'm not sure what effect failing or refusing an NSA polygraph might have on any security clearance granted by any other government agency.

For related reading, see "Use of the Polygraph in Security Clearance Investigations" (Chapter 8 of Security Clearances and National Security Information: Law and Procedures by Sheldon I. Cohen, December 2000).