From which database?

You can "pass" an NCIC check (not NCIS which is for FFLs-- it has nothing to do with this discussion really-- NCIC is for LE) with no conviction recorded in NCIC but have an arrest recorded in NCIC. Then the facts of that arrest can be looked into and you can be found ineligible for whatever clearance you are seeking based on the facts of the arrest (eg. a plea of no contest which didn't result in a "conviction" per se, but you were guilty of the crime). But with proper expungement, even the arrest is removed (expunged) from the NCIC database.

So I ask you, if not NCIC, what database does this secret retained data come from? How do you know that the people you know who have "passed" NCIC checks but failed to get security clearances didn't suffer from the arrest/conviction issue I described above. Bear in mind that for an arrest to be expunged from NCIC, the proper inter-agency procedure has to be followed and it doesn't always happen.