James Comey – not Bernie Sanders -- is the biggest challenge to Hillary Clinton’s presidential ambitions, a prospect that should keep the former Secretary of State up at night. The fiercely independent head of the FBI is directing the investigation into Clinton’s use of a personal email server and attendant issues raised during the Benghazi inquiry, which could lead to indictments of the former Secretary of State or her various aides.

If the probe determines that Hillary or her aides mishandled classified information or obstructed justice, her campaign will likely collapse. (Hence, the rumored possibility that Joe Biden could still emerge as a “draft” candidate.)

Related: Clinton Emails Contained Classified Material: U.S. Inspector

Comey has shown a nettlesome tendency to stray off the Obama reservation. Most recently, he challenged White House orthodoxy by linking the rise of homicides around the country to stepped-up scrutiny of the police. In a speech at the University of Chicago Law School last week, Mr. Comey described the “YouTube” effect that has created a “chill wind blowing through American law enforcement over the last year.” Police, he suggested, are so concerned about starring in a video that goes viral that they are attacking their job more tentatively to the detriment of law and order. The New York Times reported that Comey’s remarks “caught officials by surprise at the Justice Department, where his views are not shared at the top levels.”

Comey has also parted ways with Obama on the ‘Black Lives Matter’ controversy. In his speech in Chicago, the FBI director declared that “all lives matter” three times; at the White House, Obama was simultaneously defending the Black Lives Matter mantra while participating in a panel on criminal justice reform. The president helpfully explained that the protesters use the phrase ‘black lives matter’ “not because they said they were suggesting nobody else’s lives matter; rather, what they were suggesting was there is a specific problem that is happening in the African American community that’s not happening in other communities. And that is a legitimate issue that we’ve got to address.”

Comey has a reputation for integrity, a quality lauded by President Obama when he nominated the former Deputy Attorney General for his current post. Obama told how Comey prevented an ill Attorney General Ashcroft from being hoodwinked into reauthorizing a warrantless eavesdropping program, in the process standing up to President George W. Bush and putting his career on the line.

"He was prepared to give up the job he loved, rather than be a part of something that he felt was fundamentally wrong," Obama said.

Related: Emails Show Hillary Had Secret Benghazi Warning

That dogged quest for justice and independence streak may come to haunt Hillary Clinton. Comey’s credibility expands when he warns Americans to be “deeply skeptical of government power,” as he did in a 60 Minutes interview. He cautioned, “You cannot trust people in power,” noting that the “founders knew that. That’s why they divided power among three branches, to set interest against interest.” Pressed to reassure the nation about the FBI’s surveillance activities, Comey confirmed “The promise I’ve tried to honor my entire career, that the rule of law and the design of the founders, right, the oversight of the courts and the oversight of Congress will be at the heart of what the FBI does.”

Comey appears fearless. As a kid, he was held hostage by a gunman during a home invasion; with his younger brother, he escaped twice, only to be caught again. This is the kind of straight arrow that Mrs. Clinton does not want on her case, and that Attorney General Loretta Lynch may not be able to corral. Asked by Scott Pelley during the 60 Minutes piece whether he didn’t have a duty to support President Bush on the eavesdropping matter, Comey answered, “No, my responsibility, I took an oath to support and defend the Constitution of the United States.”

What could bring Hillary down? According to some who have followed the case closely, Mrs. Clinton could be charged with breaking several laws, including willfully transmitting or retaining Top Secret material using a private server, unauthorized removal of classified information from government control or storing such information in an unauthorized location, lying to Congress, destruction of government property (wiping the server), lying under oath to a judge about having given the government all her emails or obstruction of justice.

Related: The Five Big Questions Hillary Left Unanswered

This last misdeed seems particularly dangerous for Clinton. On September 20, 2012, nine days after the attack in Benghazi that left four Americans dead, Jason Chaffetz, chair of the House Subcommittee on National Security, Homeland Defense and Foreign Operations (part of the committee on Oversight and Government Reform), requested from then-Secretary of State Hillary Clinton all documents related to the Libya event. The broad request included all records, including emails. For a year, the State Department responded in dribs and drabs to the request; notably, no emails were handed over. A frustrated Oversight Committee finally (in August 2013) issued two subpoenas – one covering the initial documents request and another for the results of the internal investigation that exonerated Clinton.

It was not until August 2014 – nearly two years after the attacks and the first request for documents -- that the first Clinton emails appear, and that Congress becomes aware of the existence of her private server. Only in February 2015 is Congress alerted that Clinton has only made available some of her records. Shortly thereafter, The New York Times breaks the story that Hillary has turned over 55,000 pages of emails and more subpoenas follow. The obfuscation only worsens, as she claims to have destroyed some 30,000 “personal” emails, despite a Congressional “preservation letter” telling her to protect any records.

Justice Department investigators and the FBI are reviewing Clinton’s explanations and behavior. We will know in the next few months whether she or her aides will face charges. Republicans are skeptical that Obama’s Justice Department will prosecute any misdeeds discovered to have been perpetrated by his former Secretary of State and the likely Democratic nominee. With James Comey leading the investigation, and unlikely to participate in any cover-up, they should have faith in the system.