Nick Penzenstadler

USA TODAY

FBI agents interviewed Hillary Clinton for about 3 ½ hours Saturday morning at their headquarters in Washington, steering the probe into her private email server closer to an expected conclusion in coming weeks.

Clinton, who left office as Secretary of State in February 2013, used a private email and server hosted at her home in New York — inconsistent with long-established policies governing all federal agencies.

Clinton, the presumptive nominee on the Democratic ticket for president said the system was “absolutely permitted” and commonplace for private communications. But an independent State Department inspector general report in May said the use was not appropriate largely because it didn’t comply the Federal Records Act and was vulnerable to hackers.

FBI, Clinton talk for 3½ hours over emails sent on private server

Private interest groups sued for the emails under the Freedom of Information Act and congressional committees pushed for answers, but the case took a serious turn when it was referred to the FBI in July 2015. FBI agents will consider the classified material involved and determine if it was a crime to handle the documents in that manner.

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The scandal has dogged Clinton and drew headlines again this week after former president Bill Clinton met with U.S. Attorney General Loretta Lynch on a tarmac in Arizona. Lynch was on the defensive Friday afternoon at a convention in Colorado and said she will accept the recommendations of the probe.

What happens next?

Investigators will wrap up their case in coming weeks by comparing Clinton’s interview Saturday to other pieces of their probe.

Since Lynch appears to be taking a lesser role given the attention from her impromptu meeting in Phoenix, more attention may be paid to career prosecutors at the Department of Justice involved in the case and FBI Director James Comey, a Republican.

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The FBI must decide on an official recommendation on a formal indictment — which Lynch pledged Friday to support. The key question is whether the server and Clinton’s conduct breached the legal standards for mishandling classified information.

Some spectators have compared the decision to whether to hit former CIA Director David Petraeus with felony charges for his own mishandling of classified information. While the FBI reportedly requested those heavier charges that could carry prison time, then-Attorney General Eric Holder downgraded the charges to misdemeanors.

What if the DOJ indicts Clinton?

A federal indictment would send unprecedented shockwaves into the election.

An indictment itself wouldn’t technically disqualify Clinton from running, obtaining the party’s nomination or winning the election in November. But she would face enormous pressure to step aside whether the indictment comes before or after accepting the party’s nomination in Philadelphia at the end of July.

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If the indictment happened before the convention and Clinton withdrew, it would lead to a scenario where delegates could be unbound and switch affiliations. But that wouldn’t automatically mean a Bernie Sanders nomination — it could be another Democrat that’s been in the race, or a new contender.

An indictment after the convention—and a potential new candidate would be unchartered territory — and observers say Clinton’s vice presidential pick could pick up the banner.

If the FBI recommends an indictment, Lynch will likely appoint a special prosecutor to the case.

What if Clinton faces no indictment?

Despite emerging from the legal cloud rumbling over her campaign, the investigation is sure to haunt Clinton through November, and likely beyond.

There’s a scenario where Clinton herself doesn’t face a grand jury, but several of her top aides like Cheryl Mills and Huma Abedin, now trusted campaign confidants, could be charged.

It’s possible the FBI recommends an indictment, and despite Lynch’s assurances, she declines to charge, or reduces the charge.

That scenario would likely lead to high profile resignations, given the political overtones.