But with the new year, there's the possibility some of these questions will finally be answered.
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There are already scheduled hearings and deadlines in former Trump campaign chairman Paul Manafort's criminal cases and a growing expectation of the wind-down of Mueller's work and use of a federal grand jury.
Here are 16 questions about what's to come in the Russia probe:
How does the Mueller investigation end?
When he concludes his work, Mueller must provide a confidential report to the attorney general. But before that happens, he could seek additional indictments. So far, Mueller's team has secured guilty pleas from seven people, including President Donald Trump's top two campaign leaders, his former personal attorney and his first national security adviser. Twenty-six others, who are all Russian, have been indicted by Mueller.
In theory, the special counsel will answer a cascade of questions raised in the investigation, including whether he believes Trump obstructed justice, and will release findings on the allegations of coordination between the Trump campaign and the Russian government. Mueller will likely assess whether Trump knew in advance about the Trump Tower meeting with Russians in June 2016, whether campaign contacts sought stolen Democratic Party emails, whether foreign money illegally came into the election and what gave rise to the Republican Party changing its platform on Russian intervention in Ukraine.
Will the public see Mueller's findings?
Whether Mueller's findings will become public and how is another question entirely -- one that could lead to a fight of its own. If Mueller and the Justice Department do not make the report public -- and if the White House wants to keep it largely secret -- Congress could issue a subpoena to try to force its release.
Some details may be held back, because of assertions of executive privilege, grand jury secrecy and other confidentiality considerations. Congress and public interest groups could go to court over what should be released.
Will Trump fire Mueller?
From almost the beginning, the threat that Trump or the attorney general could fire Mueller has hung over the probe. But Trump hasn't done it -- yet.
Speculation about Mueller's impending dismissal reached a fever pitch last April, after multiple news organizations, including CNN, reported that Trump was furious over the probe and previously directed his White House counsel to fire the special counsel. Don McGahn, who was then the White House counsel, refused.
Now McGahn has left the West Wing, as has chief of staff John Kelly, who presided during much of the time Trump railed against Mueller. Attorney General Jeff Sessions, who recused himself from overseeing the investigation, left the Justice Department in the hands of now-acting Attorney General Matthew Whitaker, who disregarded the advice of a Justice Department ethics official and did not recuse from the probe. The next boss in line to oversee Mueller is Bill Barr, who was attorney general during the George H.W. Bush administration and is again nominated to be attorney general.
Barr's approach to Mueller is yet to be seen. Previously, he wasn't completely supportive of the investigation. He wrote a memo to Justice Department officials in June arguing that an obstruction of justice inquiry into Trump's decision to fire FBI Director James Comey was "fatally misconceived."
Will Mueller interview Trump?
It's unclear if Mueller has more questions for Trump. The President's team has signaled for months that it would fight if he were asked to testify under subpoena or sit for an interview with Mueller, two situations where lying can be prosecuted as a federal crime.
Instead, the President's defense team held off a court fight by responding in writing to a set of questions from Mueller just before Thanksgiving. They dealt largely with the allegations of Russian collusion and the time period before the inauguration.
But Mueller's team has always been interested in interviewing the President, and the two sides have been in communication as of last month.
If Mueller did send Trump a subpoena for grand jury testimony, historical legal precedent suggests Trump would have to answer questions under oath.
Trump was the chief critic of Mueller in the second half of 2018, calling the investigation a politically motivated witch hunt repeatedly and at a frantic pace.
"The Russian Collusion fabrication is the greatest Hoax in the history of American politics," Trump tweeted on December 29.
How long will Mueller's grand jury continue to meet?
The grand jury used by Mueller to indict Manafort, his deputy Rick Gates and 26 Russians over the past year and a half first assembled in the Washington federal courthouse in the summer of 2017. Its initial 18-month term was extended by up to six months on Friday.
The grand jury has convened on most Fridays, receiving scores of witnesses who gave testimony and hours of findings from prosecutors about the intricacies of Russian attempts to infiltrate US politics.
This secret body of no more than 23 citizens is a powerful tool Mueller can use to compel evidence collection and bring in witnesses. It's also the panel of peers that ultimately votes to approve criminal indictments.
Apparently, it's still doing its work.
The grand jury last gathered on December 21, according to CNN reporting.
Mueller also has the option to present evidence to other established grand juries, such as the one in Virginia he used to open a second case against Manafort.
What about House Democrats?
Beyond Mueller, a new class of investigators was sworn in this week: House Democrats.
Democrats now control the key House committees that can investigate Trump's campaign ties to Russia, his personal finances, obstruction of justice and just about everything in between. These committees have subpoena power and can force key witnesses to turn over sensitive documents, and can demand that Trump's closest allies appear for public hearings to face blistering questions in front of the cameras.
Senior Democrats have said they won't wait for Mueller to complete his probe before launching their own investigations. Though some staunch liberals are clamoring for impeachment, Democratic leaders including House Speaker Nancy Pelosi say that won't be on the table until Mueller closes shop. Even if Mueller does wrap up his work in 2019, Democrats are sure to keep up the pressure with their aggressive moves on the Hill.
Will Roger Stone's associate be forced to testify?
The US Court of Appeals for the District of Columbia Circuit has not yet ruled on Stone associate Andrew Miller's attempt to dodge a subpoena and his challenge of Mueller's authority. Miller lost his case before a trial-level judge and was held in contempt of court, then appealed. If he wins, the court could undercut Mueller's appointment within the Justice Department. But if the appeals court sticks with the trial judge's findings and Miller still refuses to testify, he could go to jail.
Miller is one of 13 known Stone associates who've been approached by investigators.
What mystery foreign-state-owned company is trying to hold off a subpoena?
A second grand jury subpoena challenge related to the Mueller investigation has worked its way to the Supreme Court in recent weeks. That challenge, from an unnamed foreign-government-owned company, is fending off mounting fees for failing to turn over information to the grand jury. As of Friday afternoon, the Supreme Court was still considering whether to freeze the fine.
What are the 'several ongoing investigations' Gates is still helping team Mueller with?
Last we heard from Gates, he had testified for three days against Manafort at trial and "continues to cooperate with respect to several ongoing investigations," his defense lawyer and Mueller's prosecutors said in November. It's notable that prosecutors' status report on Gates hasn't hinted at a coming sentencing, given prosecutors' successful convictions of Manafort. What else could the top Trump campaign and inaugural official be helping Mueller and the Justice Department with?
The next status report from prosecutors and Gates' legal team is scheduled to be submitted to the court on January 15.
Will powerful Russians get access to national security investigation secrets?
The Russian company Concord Management and Consulting is fighting this battle in court, as it fends off a criminal indictment for allegedly funding a social media conspiracy to disrupt the 2016 presidential election. Concord has taken a scrappy, antagonistic approach to Mueller's allegations in court.
Concord was the only Russian company or person out of 15 total to fight the propaganda charges -- it pleaded not guilty and the oligarch who owns the company has lambasted the allegations as a joke.
The company previously lost in its requests for the court to invalidate Mueller's indictment and authority. Now, its request to access and to share "sensitive" evidence in the case among Russians gets to what prosecutors believe is the heart of its strategy. Prosecutors say it's particularly risky for Concord to get evidence in the case because of its ties to indicted and sanctioned Russian oligarch Yevgeniy Prigozhin. The judge has yet to decide.
How important is Konstantin Kilimnik?
Over and over again, one name -- Konstantin Kilimnik -- has been connected to several parts of the Mueller investigation. Could Kilimnik be at the heart of Mueller's pursuit?
Kilimnik surfaced first last year in the case against Dutch lawyer Alex van der Zwaan, when Mueller's team admitted it cared about how van der Zwaan had connected with Kilimnik and Gates in fall 2016.
They also said Gates knew Kilimnik worked for the Russian military intelligence agency, GRU, which Mueller alleges hacked the Democrats in 2016.
Most recently, Mueller's team acknowledged it had asked Manafort several things about Kilimnik and their meetings, and it said Manafort had lied to the prosecutors about his contact with his longtime foreign colleague. Though the Justice Department has not said it yet publicly, Kilimnik met with Manafort twice during the Trump campaign and helped Manafort offer a Russian oligarch briefings on the election, according to reports from other news organizations and Manafort's and Kilimnik's public statements.
Another cooperator in the Mueller investigation, lobbyist W. Samuel Patten, also had contact with Kilimnik through 2017, as they secured tickets to the Trump inauguration for a paying Ukrainian oligarch client.
Like Gates, Patten's cooperation with the special counsel's office has stayed under wraps and apparently continues.
Mueller indicted Kilimnik last year for attempting to tamper with potential witnesses in Manafort's case, and said he had worked with Manafort and Gates to "carry out the criminal schemes" to which Manafort has admitted. The question remains: What else have they learned about him?
Because he lives in Russia, Kilimnik has not yet appeared in US court to enter a plea. He has not publicly responded to the obstruction charges. In interviews, he has denied working for Russian intelligence.
How many years will Manafort serve in prison?
A prison sentence is a near certainty.
The former Trump campaign chairman and lobbyist will go before federal Judge T.S. Ellis on February 8 for his first sentencing on eight tax and bank fraud convictions. And, following a broken plea deal, Manafort is scheduled to be sentenced by a second judge about a month later for additional crimes, though this date may be pushed back.
Before then, the public may learn more about Manafort's lies to prosecutors during his nine cooperation sessions with Mueller's office, which began after he pleaded guilty to avoid a second trial. Manafort has lived in jail since June, when prosecutors accused him of attempted witness tampering. The possibility that prosecutors would ask for leniency for Manafort has evaporated.
The mounting convictions set Manafort up for a decade or more of prison time. His prospects look bleak.
However, Manafort has one Hail Mary he can still pray for: a pardon from the President.
What did Michael Cohen tell prosecutors?
This is what special counsel office prosecutor Jeannie Rhee said at Michael Cohen's criminal sentencing in December: "He has provided our office with credible and reliable information about core Russia-related issues under investigation and within the purview of the special counsel's office."
What could those "core Russia-related issues" be? It's not yet clear whether Cohen's assistance will boost other threads of the investigation.
Mueller's team said in an earlier court filing that Cohen spoke to investigators about communication efforts between the Trump campaign and the Russian government in 2016 and about his contact with White House officials in 2017 and 2018.
They also indicated that Cohen was in touch with White House staff and Trump's lawyers while he prepared a written false statement to Congress, for which he was criminally charged.
The Justice Department instructions for Mueller's investigation put the Russian government's efforts to interfere in the 2016 presidential election at its core.
Will Julian Assange ever leave the Ecuadorian Embassy?
The Ecuadorian government has signaled unhappiness with its guest of almost seven years at its London embassy -- setting up a will-it-or-won't-it scenario that could force Assange into US authorities' custody. Assange originally stepped inside the embassy in 2012 while wanted for questions over sexual assault allegations in Sweden. He's maintained his innocence, and since then has become a focus in Mueller's investigation of the Russian hack and public distribution of the Hillary Clinton campaign emails and information from Democratic Party computers in 2016. Justice Department investigations of Assange and his outlet WikiLeaks date to at least 2010, when the site posted files from former US Army intelligence analyst Chelsea Manning.
Recently, US prosecutors -- in an apparent slip-up -- mentioned in a court document that Assange has been charged in a still-secret federal court case. It's not yet known what he's been charged with, or if the case relates to Mueller's investigation at all.
What do prosecutors intend for Roger Stone?
Several signs for months now have pointed toward a grand jury investigation into Roger Stone's alleged pursuit of stolen Clinton and Democratic documents and his alleged communications with WikiLeaks.
That Mueller has called upon Stone associates for information, documents and grand jury testimony is the most obvious part.
The Mueller team also mentioned an unnamed person -- believed to be Stone -- in describing Russian hackers' contacts with Americans around the time they were releasing damaging Democratic emails in 2016. Stone bragged about close ties with Assange during the 2016 campaign but then revised his story and said he was just repeating publicly available information.
The fullest account of Stone's actions in 2016 came in draft court filings and text messages Stone associate Jerome Corsi shared with CNN in November. Corsi says Mueller presented him with the option to plead guilty to a lying charge, but he rejected the deal. The draft filings from November describe how Stone allegedly pushed his associates to get stolen Democratic documents from WikiLeaks before they went public.
Two weeks ago, the House Intelligence Committee agreed to send Mueller transcripts of a 2017 closed-door interview with Stone, indicating his statements to Congress about the Russia investigations are at the heart of the special counsel's interest.
Stone has not been publicly charged with a crime. He has said he believes he will be indicted, and he has asked his online supporters to help his legal defense.
What's next for Michael Flynn?
In one of the more dramatic courtroom moments of 2018, Michael Flynn was encouraged by a federal judge to delay his sentencing and cooperate further with the government.
Mueller's office had asked for no jail time for the former national security adviser after he provided the Justice Department with "substantial assistance" in investigations, yet federal Judge Emmet Sullivan was clearly incensed that the former high-ranking military and intelligence leader had lied to the FBI in his first days in the Trump administration.
Will Flynn ultimately go to prison, like the four Mueller defendants who have already been sentenced? And is there more he can do to help the Justice Department and Mueller's team before he appears before Sullivan again? His next in-court update is due on paper in mid-March.
For all of the above topics, the special counsel's office declined to comment.