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(CNN) —  

With the recent criminal indictment of 12 Russian intelligence agents, the special counsel’s office made clear it has a treasure trove of information for its investigation into Russia’s interference in the 2016 presidential election. What’s less obvious is how long Robert Mueller will continue his work.

The indictment could be the high point for his team. Or it could be simply the crest of one of several coming waves.

An investigative interview of President Donald Trump, likely regarding Mueller’s probe into whether the President obstructed justice, still hangs in the air. So do the legs of the investigation involving former campaign chairman Paul Manafort’s role on the campaign, and involving former national security adviser Michael Flynn’s cooperation with investigators.

There are already some signs that Mueller’s office is prepared for an ultimate wind-down. Prosecutors from the US Attorney’s Office in Washington and the Department of Justice’s national security division are working on cases brought by Mueller, signaling that they’ll see them through if the special counsel’s office disappears before the court actions conclude.

And federal prosecutors in Manhattan separate from Mueller are handling the investigation into the president’s former personal attorney, Michael Cohen, which may touch on payments to women with whom Trump allegedly had extramarital affairs during the campaign.

Even so, Mueller still appears to be shepherding several related investigations that Deputy Attorney General Rod Rosenstein laid out in a memo for Mueller last August. The memo appears to describe the scope of the investigation point by point. Almost a full page of the discussion of Mueller’s scope is still hidden from public view.

Yet some parts of the still-secret investigation have become evident.

The President

Chiefly, there’s no conclusive public finding yet into whether Trump intended to obstruct justice or knew of illegal coordination — if there was any – between his campaign and the Russian government.

A conclusion may not come before the end of the year, given the timing of the midterm elections.

Under Justice Department custom, prosecutors generally avoid overt investigative steps and returning indictments against a candidate for office within 60 days of an election. That rule is not set forth in any official policy or regulation, however. Mueller could always ask Rosenstein for an exception. Or he could look at the example of former FBI Director James Comey, who was roundly criticized for making a statement on the investigation into Hillary Clinton’s emails 11 days before the 2016 presidential election.

One investigative step that appears to be in Mueller’s plan is interviewing the President.

The possibility of an investigatory interview with Trump has haunted the Oval Office for half a year now, as the President’s then-attorneys John Dowd and Ty Cobb, and later Rudy Giuliani and others, have gone back and forth with Mueller.

If the two sides cannot reach an agreement, a grand jury subpoena to force Trump to talk could be in the works. That would likely lead to a fight over presidential power under the Constitution — and may end up at the Supreme Court.

Perhaps Mueller doesn’t need Trump on the record. He already has dozens of witness interviews, plus hundreds of Trump’s own tweets, public speeches and on-camera interviews.

If Mueller chose not to indict the President, he will likely present his findings in a report to Congress. That could include a recommendation to impeach Trump.

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Flynn still helping

Former national security adviser Michael Flynn cut a plea deal with investigators last December. There has been no apparent conclusion to that part of the investigation, and the amount of information Flynn has given them hasn’t yet become public.

Flynn has spoken with prosecutors about his conversations during the presidential transition. Those conversations relayed details from the Russian ambassador to senior Trump campaign officials including Jared Kushner, according to his charging documents.

At a court appearance last week, a federal judge made clear Flynn hasn’t been sentenced yet for lying to investigators because he continues to cooperate with prosecutors. That signals that more criminal cases related to what Flynn knows could be coming.

Manafort fears more

Former Trump campaign chairman Paul Manafort has been charged on crimes related to his Ukrainian lobbying and financial disclosures. Manafort says he is not guilty and is awaiting two trials, with the first set to start July 25.

Rick Gates, Manafort’s longtime deputy and another top Trump campaign and inauguration official, hasn’t appeared in public since he pleaded guilty in February to lesser charges than he first faced. Gates is now helping Mueller’s office, likely with the prosecution’s cases against Manafort.

He could also be contributing to other parts of the investigation. Mueller’s team initially sought Gates’ help to accomplish its central mission of investigating the campaign and Russian collusion, CNN reported in March.

Prosecutors haven’t yet said publicly what they’ll do with Manafort’s Russian connections during the campaign. His attorneys have said in court they believe Mueller continues to investigate him.

Russian threads

Then there are the Russians. The hack of the Democratic Party and Clinton campaign during 2016 fell into Mueller’s purview from the start. Those charges surfaced July 13, when Mueller’s team indicted 12 Russian military intelligence agents for their alleged conspiracy. But several unnamed people in the indictment – including a congressional candidate who allegedly asked the Russians for stolen emails, plus entities that appear to be WikiLeaks and Trump adviser Roger Stone, who communicated with the hackers – haven’t been charged.

Mueller’s team also said in a court filing late Monday night that even before Mueller started work last May, federal officials were looking into another group of Russians. Those Russians, a team of Russians and Russian companies that distributed anti-Hillary Clinton propaganda over social media, have since been charged.

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Stone: Think I'm probably person in indictment

What else?

That leaves several possible threads that Mueller’s office has pulled on and have yet to resolve. What will become of the case about Stone, who’s had several of his associates testify before Mueller’s grand jury? CNN reported that Mueller’s team has been in a court tangle with the attorneys of a former employee of Stone’s. Their hour-and-a-half-long sealed hearing on July 18 suggests the grand jury investigation of Stone presses on.

Is there more to George Papadopoulos’ dealings with the campaign that Mueller will pursue? The public will likely learn more in September about Papadopoulos’ cooperation with the special counsel’s office, in advance of and when he is sentenced. Papadopoulos pleaded guilty to lying to investigators about his contacts with Trump campaign officials and suspected Russian agents. While he worked on the Trump campaign and before the hackers leaked their stolen materials, Papadopoulos reportedly learned the Russians could offer “political dirt” on Hillary Clinton. That hasn’t yet tied back to Mueller’s case against the hackers who distributed that “dirt.”

Finally, what did Mueller find about that June 2016 Trump Tower meeting between the top campaign officials and Russians?

A definitive end?

In the court papers Monday related to the Russian troll farm, Mueller’s team wrote about how their investigation will reach a definitive end.

When it does, Mueller will have to provide Deputy Attorney General Rod Rosenstein a confidential report explaining his decisions to prosecute or not to prosecute. Rosenstein gets to sign off on every potential criminal case and would have to tell Congress if the Justice Department decides not to pursue a case the Mueller’s office recommends.

Mueller’s team acknowledges that their work could always be cut short – if Rosenstein makes it so. Mueller could be fired for misconduct or “good cause,” such as violating Department of Justice policies, or Rosenstein could choose to end the investigation.

There’s one more way for Mueller’s investigation to naturally end: If Rosenstein wants, he could let it expire with the end of the federal government’s fiscal year, which is September 30, according to the court filing.

“Special counsels appointed under the regulation can be expected to have a limited time horizon and the investigation a definite endpoint,” the prosecutors wrote. “The lifespan and scope of the investigation at all times stay within the [acting] Attorney General’s control.”

CNN’s Laura Jarrett and Gloria Borger contributed to this report.