Get a cup of coffee, it's long but worth it. The timeline is non-partisan and sticks to the facts, basically it is alt-right/trump troll/conspiracy free.
Bottom line: It doesn't look good at all.
October 28, 2014: The State Department formally asks Clinton for all of her work-related emails.
December 5, 2014: She turns over 30,000 emails from her @clintonemail.com account to the State Department. Another 31,000 emails from the same account were deemed personal, and Clinton kept those. Her lawyers did the sorting, no State Department or National Archives personnel had a chance to appraise or examine the remaining 31,000.
December 2014: Shorty after turning the 30,000 emails, Clinton decides she no longer needs access to any of her emails older than 60 days. Her staff is told to change the retention policy on her server, which will lead to the deletion of all her the emails that weren't turned over to the State Department.
The FBI later recovered about 17,500 of Clinton’s “personal” emails. FBI Director James Comey has said that “thousands” were indeed work-related.
March 25, 2015 and March 31, 2015: There were two conference calls between Clinton staffers and PNR, the company managing her emails. Between those two calls, Combetta, the PNR employee managing Clinton server (and Reddit user 'Stonetear'), has an “Oh shit!” moment and remembers that he’d forgotten to make the requested retention policy change back in December 2014. He immediately deletes all of Clinton’s emails and uses BleachBit to permanently wipe them.
He later told the FBI that at the time he was aware of emails mentioning a Congressional request to preserve all of Clinton’s emails.
Sometimes in 2016: The Justice Department gives Combetta some form of legal immunity.
The FBI having Combetta take the fall for the deletions while making an immunity deal with him *could* be a particularly clever move to prevent anyone from being indicted. That part isn't clear yet.
In any circumstances, the FBI giving Combetta immunity makes no sense at all. It's the equivalent of giving a hired hitman immunity without going after the person who hired him.