FBI background checks look into a lot more than just criminal records. A person doesn't have to be convicted or even charged with something in order for it to disqualify them. Some things that aren't even considered crimes can disqualify you. Having too much debt, being an alcoholic, having a family member with too much debt. Having a history of anything embarrassing that you could be blackmailed for. Et cetera.
They ask you questions about your past and strongly encourage you to tell the whole truth, then they interview people who know you in order to corroborate your telling of it. And since the job requires a TS clearance, you have to pass a polygraph test too in which they ask you questions specifically tailored to your past as it appears in the results of your background check.
It's not a simple matter of going to the local police station and asking for your rap sheet the way civilian job interviewers do.