Special counsel Robert Mueller’s probe into potential collusion between Donald Trump’s presidential campaign and Russia handed down its biggest indictment yet on December 1, charging former National Security Adviser Michael Flynn with making false statements to the FBI.

The charge, which Flynn pleaded guilty to on Friday morning, related to an interview FBI agents conducted with him on January 24, 2017, just days after President Donald Trump took office and he began serving as his top national security aide. According to the charging document, Flynn made false statements to the FBI about his contacts with Russian Ambassador Sergey Kislayk during the transition period about whether Trump would be willing to lift sanctions the outgoing Obama administration had slapped onto Moscow.

The news is in part significant because, after previous charges against three former Trump campaign aides, this is the first against a person who actually served in the Trump administration.

But the biggest consequence for the larger investigation is that it appears that Flynn has flipped, and will begin providing information that could incriminate other associates of President Trump in the Russia scandal or related matters. That could theoretically include Trump himself; ABC News reported Friday that Flynn feels “abandoned” by Trump and is prepared to testify that the president had explicitly ordered him to talk to the Russians.

After reports in November that the special counsel had enough evidence to indict Flynn — and perhaps also his son, Michael Flynn Jr. — Flynn’s lawyers withdrew from an information-sharing agreement with President Trump’s legal team, and began meeting with Mueller’s team. It is likely that these meetings included “off the record” discussions about what Flynn could provide Mueller in exchange for leniency in charging or sentencing.

So now, it seems, Mueller has turned a former high-ranking Trump aide into a cooperating witness. But to understand how we got here you have to understand the investigation itself. Special counsel investigations are rare and legally peculiar; this one is especially complicated because the underlying scandal, over Trump’s ties to Russia, is complicated in its own right.

What follows is a clear guide to the biggest, most pressing issues about the Mueller investigation: how it works, what Mueller and his team are looking into, what we know about the Russia scandal so far, why it all matters, and what could happen next.

1) What is the Mueller investigation?

On May 17, Deputy Attorney General Rod Rosenstein announced that he was appointing Mueller as a special counsel charged with investigating connections between the Trump campaign and Russia’s effort to interfere in the 2016 election.

“The public interest requires me to place this investigation under the authority of a person who exercises a degree of independence from the normal chain of command,” Rosenstein said in the announcement.

Though various congressional committees are investigating Russian interference in the election and the Trump campaign’s potential collusion with Moscow, the Mueller investigation is where the real action is. It’s the one that can actually file federal charges. It’s also best positioned to get financial records, examine secret intelligence, and flip witnesses. When people talk about “the Russia investigation” these days, they’re usually talking about Mueller and his team.

The investigation actually started well before Mueller came on board — the FBI began it in the summer of 2016, prompted by the hacking and leaking of Democratic National Committee internal emails.

In the ensuing months, that investigation turned toward examining the broader topic of what intelligence officials identified as a Russian government campaign to interfere with the elections, and whether the Trump campaign or Trump associates were involved. Other agencies — including the CIA, the National Security Agency, and the Treasury Department’s financial crimes unit — also got involved, scrutinizing financial transactions and intercepting Russian communications.

Throughout all of that, the investigation followed the ordinary FBI chain of command. Then-FBI Director James Comey was the major figure overseeing the investigation, working with top Justice Department officials, who would in the end decide whether charges would be filed.

But on May 9, Trump fired Comey. Soon afterward, the president admitted that his unhappiness with Comey’s handling of the Russia investigation played a role in his firing. A series of leaks about troubling behavior by the president, including asking Comey to pledge his loyalty to Trump personally, made it into the press, raising serious questions about the investigation’s independence.

Enter Bob Mueller.

2) So who is Robert Mueller, anyway?

Mueller is best known for serving as FBI director for 12 years spanning the administrations of George W. Bush and Barack Obama. Sworn in just a week before 9/11, Mueller was soon tasked with overseeing the investigation into the attacks and leading the law enforcement side of the new war on terror. He was also charged with transforming the FBI into a modern intelligence agency that was supposed to prevent new attacks rather than just investigating crimes that had already taken place.

Mueller’s FBI faced outside criticism for allegedly using community outreach efforts as a pretext for collecting information on Muslim Americans. But in Washington, he gained a reputation as a principled figure — for instance, he once threatened to resign because he thought a surveillance program was being unlawfully implemented. And despite the fact that he was a Bush appointee, Obama came to regard him so highly that he asked Mueller to stay on for two extra years after his 10-year term had expired, before eventually choosing Comey to replace him.

Before his stint in the FBI, Mueller was a Marine Corps veteran who fought in Vietnam, and he then spent the next few decades going back and forth between Justice Department posts and private sector law firms. After he retired in 2013, he joined the Washington law firm WilmerHale as a partner. In his private capacity, he oversaw a major investigation into the NFL, the settlement of emissions lawsuits against Volkswagen, and another case related to Takata Corporation’s faulty airbags.

And after Comey’s firing, he was in the mix to return to his old post as FBI director — until Rosenstein appointed him special counsel instead on May 17.

3) What is Mueller currently investigating?

The investigation centers on Russian interference during the 2016 election and, as former FBI Director Comey put it, “the nature of any links between individuals associated with the Trump campaign and the Russian government and whether there was any coordination between the campaign and Russia’s efforts.”

This includes such topics as the hacking and leaks of prominent Democrats’ emails, the meeting Donald Trump Jr. set up with a Russian lawyer in June 2016, whether the campaign was involved in Russian efforts to spread fake news targeted at voters in key states, and Russian efforts to hack election-related computer systems (which do not seem to have changed any voting tallies).

However, that’s not all about. Mueller is also looking into potential criminal activity on related fronts, including financial transactions from Trump associates before the campaign, and whether the president himself has attempted to obstruct justice while in office.

So far, four people have been charged or pleaded guilty in the probe. They are:

Michael Flynn : Trump’s former National Security Adviser. On December 1, the special counsel charged Flynn with making false statements to the FBI about his contacts with Russian ambassador Sergey Kislyak during the transition. He pleaded guilty Friday to lying to the FBI and is believed to be cooperating with Mueller.

: Trump’s former National Security Adviser. On December 1, the special counsel charged Flynn with making false statements to the FBI about his contacts with Russian ambassador Sergey Kislyak during the transition. He pleaded guilty Friday to lying to the FBI and is believed to be cooperating with Mueller. Paul Manafort and Rick Gates : These are Trump’s former campaign manager and another top campaign aide, who were indicted on October 30 on a total of 12 charges, including alleged money laundering, failure to disclose their financial assets, and false statements regarding their work for the government of Ukraine and a Ukrainian political party. They have each pleaded not guilty.

: These are Trump’s former campaign manager and another top campaign aide, who were indicted on October 30 on a total of 12 charges, including alleged money laundering, failure to disclose their financial assets, and false statements regarding their work for the government of Ukraine and a Ukrainian political party. They have each pleaded not guilty. George Papadopoulos: A former Trump campaign foreign policy adviser, Papadopoulos was charged this summer with making false statements to the FBI about his contacts with Russians during the campaign.

4) How dangerous is this investigation for Trump?

Depending on what Mueller’s investigation turns up, it’s quite possible that it could end Trump’s presidency.

Special counsels have the kinds of powers typically reserved for federal attorneys. First and foremost, they can issue subpoenas ordering people to turn over relevant evidence or answer investigators’ questions. Refusing to comply with one of Mueller’s subpoenas is illegal, as is lying to his investigators. This makes it very hard for the president and his associates to simply lie to hide evidence of wrongdoing, as they often do with the media.

They also have more informal ways of forcing the Trump administration to comply. For example, CNN reported in June that Mueller told the Trump administration to hold on to whatever documents they have concerning Donald Trump Jr.’s infamous June 2016 meeting. This isn’t a formal subpoena, but destroying those documents after being specifically told to hold on to them would put the administration officials responsible in danger of an obstruction of justice charge down the line.

Press reports about the investigation have definitely been embarrassing for the administration. But the ultimate purpose of the investigation isn’t to make Trump look bad, though that’s an inevitable side effect. Mueller’s formal mandate, as outlined by Deputy Attorney General Rosenstein, is to uncover any evidence of actual crimes related to the Trump campaign’s links to Russia — and to seek an indictment of anyone responsible if the evidence supports it.

There are basically three kinds of crimes Mueller’s team might uncover. The first is crimes directly related to the election — if the Trump team engaged in a criminal conspiracy to help hack Hillary Clinton’s email (stealing documents is illegal) or violated campaign finance laws by soliciting help from a foreign source, for example. The second kind is crimes committed during the investigation itself: witness intimidation, perjury, obstruction of justice, and the like. And the third is crimes committed by Trumpworld members even before they joined the campaign (more on this below).

If Mueller’s team does find compelling evidence that either type of crime has been committed, Mueller has the power to convene a federal grand jury and seek a criminal indictment against that person. If the grand jury signs off, that person is then arrested and charged — just like today.

Trump could soon be forced into a terrible choice. Either he risks a close associate or family member going to jail — or potentially making a deal with federal prosecutors in return for testimony that could incriminate others — or he uses the presidential pardon power to shield them from federal charges.

Going down the second route could spark a massive political conflict with Congress because of the obvious impropriety of Trump pardoning a family member or close associate for crimes committed to help him win the presidency in the first place.

Then there’s the question of what happens if Mueller finds evidence of criminal behavior by Trump himself.

It’s clear that Mueller has the legal authority to bring charges against any of Trump’s family members or associates. But there’s (yet another) legal debate as to whether it’s constitutional for prosecutors to indict the president himself on criminal charges. No president has ever been indicted on serious criminal charges by a state or federal attorney, so we have no Supreme Court precedent to answer the question — just legal theory.

Mueller would likely sidestep that whole minefield and do something that’s clearly within his powers: make a report to the House of Representatives that documents evidence of “high crimes and misdemeanors,” the constitutional standard for impeachment. If the evidence in Mueller’s report really were damning, it would put a lot of pressure on the House to begin impeachment proceedings.

In short, he can take the first step toward ending Trump’s presidency. That’s why Trump really needs to be afraid.

5) Can Trump fire Mueller? And how independent is his investigation, anyway?

Considering that President Trump already fired the FBI director in connection with the Russia investigation, many people are understandably wondering whether he can fire Robert Mueller as well.

If he wanted to, Trump probably could get rid of Mueller (some on the right are even encouraging the president to do so). It just wouldn’t be easy and could cost him several Justice Department officials (in addition to, of course, creating a massive political uproar).

Here’s why: Mueller is technically a special counsel, which is very different from, say, the role independent counsel Kenneth Starr played during the Clinton administration. The independent counsel was a special position that could not be fired by anyone in the executive branch and was instead overseen by the courts.

But after criticism that Starr and other independent counsels exceeded their mandates and were too difficult to hold accountable, the law that established the position expired in the late 1990s and was never renewed.

What replaced it was the special counsel position, which was established by Justice Department regulation rather than law. A special counsel is essentially intended to be an outsider who would feel less pressure to carry water for Justice Department bosses (like Mueller, a well-regarded lawyer near the end of his career).

And per the regulation, only the attorney general can fire the special counsel — and only for “misconduct, dereliction of duty, incapacity, conflict of interest, or for other good cause.”

Due to Attorney General Jeff Sessions’s recusal from all campaign-related investigations, Mueller is instead reporting to Deputy Attorney General Rod Rosenstein. In congressional testimony in June, Rosenstein said he interpreted the regulation to mean that he is the only person in government with authority over Mueller’s hiring and potential firing — not Trump and not Sessions. Furthermore, he said that he would only fire Mueller for “good cause,” and would refuse to carry out an order to fire him if good cause were not established.

However, Trump does have the authority to fire Rosenstein himself — or Rosenstein could resign if given an order to fire Mueller. The choice would then fall to Rachel Brand, an associate attorney general who supervises work on civil rights, environmental, and antitrust issues. She’s No. 3 in the Justice Department’s organizational chart, after Sessions and Rosenstein.

If she also refuses, Trump would have to keep going until he finally found an official willing to fire Mueller without good cause. (This is what happened during the Saturday Night Massacre, when Nixon ordered the Justice Department to fire the special prosecutor investigating Watergate. Two Justice officials refused to carry out his orders and resigned, but the third one went along with it.)

Another pesky issue is that the special counsel office is established by regulation and not law — meaning, theoretically, that the Trump administration could roll back that regulation or circumvent it in some way, since it does come from the executive branch. Even that could theoretically end up in court, though; law professor Josh Blackman has a useful rundown of the legal considerations over at the legal blog Lawfare.

But since Mueller impaneled a grand jury, it makes it more politically difficult for Trump to fire him. It signals that the investigation is a serious one, and that any move to get rid of him would unmistakably be a move to interfere with it.

6) Why is Trump accusing Mueller’s team of being biased?

The president has argued since at least June that the team responsible for investigating him is fundamentally compromised.

His argument is twofold. First, he says that Mueller was too close to Comey to be able to impartially investigate the man who fired him.

“[Mueller is] very, very good friends with Comey, which is very bothersome,” Trump said in a June Fox News interview. “The people that have been hired are all Hillary Clinton supporters. Some of them worked for Hillary Clinton. I mean, the whole thing is ridiculous, if you want to know the truth.” (An attorney for Comey told Snopes that Mueller and Comey “don’t really have a personal relationship” beyond work, and that despite some media reports, Mueller was “not a mentor” to Comey professionally.)

Second, Trump says that Mueller has hired a number of people with connections to the Democratic Party, who are therefore biased against Trump’s Republican administration. James Quarles, an attorney on Mueller’s staff, donated $33,000 to various Democratic candidates in the past few election cycles; Jeannie Rhee, another lawyer, represented Hillary Clinton personally in a suit requesting access to her private email server.

Legal experts, even conservative-leaning ones, think it’s unlikely the supposed biases actually represent a substantive problem for the investigation.

“I have zero doubt that Mueller is beyond reproach, and that his hiring decisions are entirely on the merits,” Jack Goldsmith, a Harvard law professor and the former director of the Office of Legal Counsel under George W. Bush, writes at Lawfare. “I don’t worry about the reality of bias.”

But Goldsmith worries nonetheless about “the appearance of bias.” The issue, he writes, “is not that Mueller’s decisions will be skewed by a staff that leans Democratic, but rather that this tilt will allow Trump and many others to lambaste all of his decisions as political.”

And that speaks, ultimately, to the essentially political game the president and his team are playing with these accusations.

Legally speaking, the president has a dominant hand. Trump can pardon anyone Mueller indicts and even potentially have Mueller himself fired. The only ultimate check is Congress’s impeachment power, which — given the current Congress — would mean getting a large number of Republicans in the House and Senate to vote to, ultimately, kick a Republican president out of office.

The charges of political bias, according to reports in both the Washington Post and New York Times, are designed to make the Mueller investigation seem like a Democratic witch hunt in the eyes of Republicans. If the Trump team succeeds in turning the investigation into a partisan issue, that would give them room to maneuver in the event that actual charges are filed and Trump decides that he wants to have Mueller fired or to pardon his family and friends.

“Mueller is such a straight arrow that he is probably oblivious to these ‘political’ concerns,” Goldsmith concludes. “But his work will be judged not just through the legal lens, but also through the political lens. And its success will stand in part on political factors.”

7) Why is Trump criticizing Mueller for “conflicts of interest,” specifically?

When you hear the Trump camp make its general case that Mueller is biased, you might hear a specific phrase coming up a lot: “conflict of interest,” or “conflict,” for short.

Trump, in a late July interview with the New York Times, claimed that Mueller had a conflict of interest because he interviewed for the job of FBI director after Comey was fired.

“He was up here, and he wanted the job,” Trump said. “I said, what the hell is this all about? Talk about conflicts? But he was interviewing for the job. There were many other conflicts that I haven’t said, but I will at some point.”

Former Speaker of the House Newt Gingrich, in a July 20 Fox appearance, was blunter: “The Mueller investigation has so many conflicts of interest, it's almost an absurdity.”

It’s odd for Trump and his allies to use the phrase “conflict of interest,” because it actually has a specific meaning aside from general bias — such as, for example, that Trump continues to maintain ownership of the Trump Organization despite being in charge of making economic rules that impact it.

But there’s a reason that phrase comes up: A “conflict of interest” is one of the pretexts a president can use to fire a special counsel. This is a point the Trump team is well aware of.

“President Trump’s lawyers and aides are scouring the professional and political backgrounds of investigators hired by the special counsel Robert S. Mueller III, looking for conflicts of interest they could use to discredit the investigation — or even build a case to fire Mr. Mueller,” the New York Times reported in July.

The Times also notes that “conflict of interest” has a very specific definition in Department of Justice regulations: having “a personal or political relationship” with the subject of the investigation. In this context, that would mean Mueller having such a relationship with Trump, one of his family members, or someone on his campaign staff. That does not appear to be the case.

But nonetheless, both the Times and the Washington Post report that Trump is trying to “build a case” that conflicts exist.

“The fact is that the president is concerned about conflicts that exist within the special counsel’s office and any changes in the scope of the investigation,” Trump attorney Jay Sekulow told the Post. “The scope is going to have to stay within his mandate. If there’s drifting, we’re going to object.”

So when you hear “conflict of interest,” what you’re really hearing is “here’s how we’re going to justify firing Mueller if it comes to that.”

8) Is Mueller allowed to investigate things that aren’t tied to Russia?

The Mueller investigation has clearly gone into territory that seems far afield from the immediate issue of collusion with Russia’s involvement in the US election.

The groundwork for at least part of this line of inquiry was reportedly laid by former US Attorney Preet Bharara, who was investigating Russian-linked money laundering before being dismissed by Trump earlier this year. The core case involved Prevezon, a Russian firm represented by Natalia Veselnitskaya, the Russian attorney who met with Trump Jr. in June 2016 promising dirt on Clinton.

An anonymous source of Bloomberg’s suggests that the Bharara-led investigation connects to the Trump investigation, though it’s not clear how. If true, it would raise serious questions about why Trump fired Bharara in the first place.

Mueller’s team was also looking at evidence Manafort might have been involved in money laundering schemes. He invested tens of millions of dollars in real estate properties, most notably in New York City; investigators reportedly looked into these dealings to see if they linked up to shady Russian activity. As Monday’s indictment makes clear, they seem to have found something.

That’s why the Trump camp’s finances are also an issue. And more broadly, one can make the case that understanding Trump’s and his family’s finances is necessary to figure out whether they have any untoward links with Moscow. The “Steele dossier,” a document put together by former British spy Christopher Steele that contains some of the most lurid allegations about Trump’s links to Russia, claims that the Russians have dumped money into Trump’s businesses. If that’s true, it would certainly help explain how collusion might have come to take place.

“Mueller may ... need to inquire into the finances and potential misdeeds of individuals in Trump's orbit if their finances and misdeeds relate to the Russia investigation,” Just Security’s Goodman says. “For example, if the Kremlin was aware of a misdeed and held it as leverage over the individual or if the Kremlin used financial ties to recruit an American to work on behalf of Russian interests.”

Trump and his allies, however, allege that the investigation into the president’s finances proves their charges of bias correct.

“This is a very dangerous witch hunt that Mueller keeps expanding it because he can't find anything in the original charge,” Gingrich said in his July 20 Fox appearance.

In technical legal terms, it would indeed be quite bad if Mueller started randomly investigating impropriety by Trump totally unrelated to Russia. “Mueller is authorized only to investigate Russian interference and matters directly related to that investigation, such as obstruction of justice,” Goodman says. So he really does have to make the case that his investigation links up to Russia and the election somehow.

But as the Atlantic’s Adam Serwer points out, there are lots of different ways that something can be related to the Russia investigation. And if Mueller stumbles across evidence of other crimes that seems totally disconnected, there is still an avenue for him to pursue them: get approval from Deputy Attorney General Rosenstein.

“Under the regulation that defines the jurisdiction for the special counsel, Mueller may ask Rosenstein for additional jurisdiction to pursue other matters that come to light in the course of the Russia investigation,” Goodman explains. “Rosenstein has the power to decide whether those matters may be added to Mueller's portfolio or to assign them elsewhere in the department.”

9) Okay, then — what happens if Trump does actually fire Mueller?

It would be difficult and costly to fire Mueller, but this is Donald Trump we’re talking about, and he could very well throw caution to the wind and decide to do it anyway (whether out of stubbornness or genuine fear about what Mueller might uncover).

This would have seismic implications, and mean no less than a crisis over the rule of law in the United States.

Though Trump would surely come up with some pretext (just as he initially did with Comey), the message would be loud and clear to all: The president is willing to fire anyone who dares investigate him or people close to him.

The FBI investigation would likely continue (unless Trump installs someone who shuts it down), but without Mueller at its head, it’s unclear how aggressive it would be, or who would be running it.

And the ball would be in congressional Republicans’ court to decide whether firing Mueller was a step too far for President Trump.

Partly in fear of angering their own voters, and partly because they hope to win policy victories in a rare moment of unified control of Washington, Republicans have generally either ignored Trump’s most controversial statements and moves or offered only the mildest of rebukes.

Yet several have said that firing Mueller would be going too far. “If he fired Bob Mueller, I think you’d see a tremendous backlash, response from both Democrats but also House Republicans,” Rep. Mike McCaul (R-TX) said on July 21.

"It would be catastrophic if the president were to fire the special counsel," Sen. Susan Collins (R-ME) told CNN.

“I cannot possibly imagine the president terminating Bob Mueller,” Sen. Bob Corker (R-TN) said in June. “It just cannot happen.”

But if Trump proves willing to imagine the unimaginable, and it happens, Republicans would face an enormous test.

Would they be willing to defy the president and pass legislation to ensure that the Russia scandal is investigated and the rule of law is protected in America — perhaps by reinstating the old independent counsel law and creating a special prosecutor who couldn’t be fired by the executive branch?

Or would they choose to become knowing participants in what would then unmistakably be a presidential cover-up of historic proportions?

It’s impossible to know right now. But what we do know is that the health of American democracy would depend on whether congressional Republicans decided to buck a president from their own party.