The former secretary of state's use of a private email server might not have been broken laws, particularly if her claims that she never knowingly shared information that was classified at the time holds true.
But the Justice Department's investigation, the State Department's processing and release of her emails, a House panel's separate investigation and dozens of impending lawsuits are weighing on the 2016 Democratic presidential front-runner's campaign.
News broke in March that Clinton used personal email addresses connected to a privately-owned server, rather than a government email, during her four years as President Barack Obama's first-term secretary of state.
Some previous secretaries of state -- including Colin Powell -- have also used private email accounts, but Clinton's approach was particularly controversial because it's out of step with typical government practice now and gave Clinton a major measure of control over what remains private and what's public.
Clinton's lawyers turned over 55,000 pages of emails to the State Department, and the department has since processed those -- releasing some, under a judge's orders, at the end of each month.
But she didn't hand in the server itself until last month, after five months of intense scrutiny over whether she flouted transparency laws or put government secrets at risk.
Why did she do it?
Clinton has chalked it all up to convenience, saying she preferred not to carry two phones -- one with a personal email address and one with a work email.
There's some legitimacy to that: Government BlackBerrys could only include one address.
But having her own personal server also gave Clinton -- as well as her closest aides -- much greater control over which emails were accessible under public records requests.
Clinton acknowledged, both in March when her private email use was first reported and again in Iowa last month, that it "clearly wasn't the best choice" to skip using a government email address.
What's in the emails?
It's mostly innocuous -- with Clinton asking for scheduling updates, fitting in trips to her hair stylist, checking on a strange trade dispute over gefilte fish and receiving notes about the balance of a career and a family from a top policy aide.
But the emails also offer insight into Clinton's closest contacts. Among them: Sidney Blumenthal, who sent what Clinton has said were unsolicited -- yet were clearly warmly received -- notes with advice and guidance on domestic and international politics.
Many of the emails are, in part or in full, redacted. That makes it tough to tell what behind-the-scenes policy conversations were taking place as Clinton navigated tricky international waters.
Of the 7,000 emails released by the State Department this week, 125 were retroactively classified.
Did Clinton break the rules?
There are laws intended to keep government records transparent -- but one that requires officials to transfer emails sent to private addresses onto government servers wasn't enacted until 2014, after Clinton departed the State Department.
Still, U.S. District Judge Emmet Sullivan suggested last month that Clinton violated government policy and made the process of responding to open records requests more difficult.
"We wouldn't be here today if this employee had followed government policy," he said at a hearing on one of the dozens of lawsuits over Clinton's emails.
Looming larger is the question of how classified information was handled -- the subject of a Justice Department investigation and the question that ultimately forced Clinton to turn over her private server to the FBI.
Clinton has insisted she never sent or received information that was classified at the time -- though many of her emails have been classified retroactively as the State Department has prepared them for release.
Was what she did illegal?
Probably not, said Anne M. Tomkins, the former U.S. attorney who oversaw the prosecution of Gen. David Petraeus over his having showed classified materials to his mistress and biographer.
Tomkins wrote this week in USA Today
that Clinton committed no crime because she didn't "knowingly" share classified materials.
"Clinton is not being investigated for knowingly sending or receiving classified materials improperly," Tomkins wrote.
"Indeed, the State Department has confirmed that none of the information that has surfaced on Clinton's server thus far was classified at the time it was sent or received," she wrote. "Additionally, the Justice Department indicated that its inquiry is not a criminal one and that Clinton is not the subject of the inquiry."
What's classified, when was it made classified and why?
All government agencies are responsible for determining which of their own materials are classified.
But Clinton's emails are being reviewed by a team of about 12 interagency officials, who are making recommendations on what should and shouldn't be classified.
State Department spokesman John Kirby told reporters in August that "there's an exhaustive, extensive review process for each and every email, which includes not just State Department reviewers going through them but having intelligence community reviewers with us at the time as we go through them in real-time to help make determinations."
Kirby added, "Some of those determinations are fairly easy -- yes or no. Some of them require additional review and discussion."
What's next? What does this have to do with Congress? Are there lawsuits over the emails?
It's not just the State Department's email releases forcing fresh headlines about the issue.
The House's Benghazi committee chaired by Rep. Trey Gowdy is calling two top Clinton aides in for closed-door depositions this week. Cheryl Mills, Clinton's State Department chief of staff, will appear Thursday, while policy adviser Jake Sullivan is expected Friday.
Another former State Department employee Bryan Pagliano who worked on Clinton's private email server has informed Congress
that he will invoke the Fifth Amendment to avoid testifying before the House Select Committee.
Clinton herself will appear before the committee for an open hearing -- one likely to attract the most television cameras of any congressional hearing in recent memory -- on Oct. 22.
There are also dozens of lawsuits seeking Clinton's emails. They range from news organizations like Gawker and The Associated Press to conservative groups like Judicial Watch.
The State Department said Tuesday that it will ask for all of those lawsuits to be consolidated under a single judge.
What's it mean for 2016?
Among Clinton's biggest challenges in the presidential race is demonstrating her authenticity -- and part of that is showing voters she's trustworthy.
Increasingly, though, voters say they distrust Clinton. The numbers have shifted dramatically since news of her private email server was first reported in March.
Her campaign has shifted tactics in recent weeks, dropping the jokes Clinton had cracked about what she'd once portrayed as a non-issue and sending aides out in an attempt to diffuse the issue in television appearances -- signaling that it's an increasingly serious challenge.