I applied for an internship with the NSA. My understanding of the process (years ago, pre-Snowden) was that they did a pass on your resume (I can't recall if there was even a phone screen), then they started background checks and if there were N internships the first N people to pass the security clearance were selected.

They went through the standard stuff, interviewing my neighbors, etc. Then they flew me to Fort Meade for a polygraph. This article matches my experiences well - the interviewers latched on to arbitrary accusations and threw them at you over and over. I walked out feeling absolutely miserable and the examiner still claiming I was hiding past crimes and drug use (nope, I confessed to everything all the way down to grabbing coins out of the fountain at the mall when I was quite young). My interviewer said some large percentage of people fail their first and most pass the second.

...except there was no second, because shortly after I passed an interview and got an internship at a large tech company that paid significantly more and didn't require me to take a polygraph. No regrets on that decision.