My understanding is that the actual FBI investigation is looking to see if there were leaks, where those leaks originated if there were, and if so, was it a matter of simply poor management or was it criminal negligence.
Near as I can tell the FBI investigation has less to do with politics than with policy. The State Department - judging by the fact that Clinton was not the first Secretary of State to use a private email/server for communication - has had a less than robust policy regarding handling of sensitive information. The FBI is trying to ferret out if there was an actual security breach as a result.
It arose out of the endless Benghazi investigations by the Permanent Committee To Impeach Anyone Named Clinton (a continuously operating part of Congress since 1992) much in the same way that an investigation into real estate led to the discovery of Bill's cigar peccadilloes.
The FBI investigation will be over soon, it doesn't look like Secretary Clinton will be charged with any wrongdoing, and there might not even be any indictments.
If Clinton wins in November, rest assured the impeachment proceedings will start on January 21st of next year.