Special counsel Robert Mueller, in the first prosecutions in his federal investigation into Russia's interference in the 2016 presidential election, filed criminal charges on Monday against two senior aides to President Trump's campaign and revealed that a third had already pleaded guilty.

A federal grand jury charged that Trump's former campaign chairman Paul Manafort and his associate Rick Gates worked secretly to influence the U.S. government on behalf of pro-Russian factions in Ukraine, then laundered their profits through a series of overseas businesses and bank accounts. In another case unsealed Monday, former campaign foreign policy adviser George Papadopolous pleaded guilty to charges that he lied to FBI agents about his meetings with a professor he knew was tied to the Russian government who offered him "dirt" – in the form of "thousands of emails" – on Trump's election opponent, Hillary Clinton.

Both pleaded not guilty to the charges during a brief appearance in federal court on Monday afternoon. Describing both men as flight risks because of their connections overseas, prosecutors sought a $10 million bond for Manafort and a $5 million bond for Gates.

While Mueller stopped short of alleging that Trump's campaign colluded with Moscow during the election, the filings are first allegation by prosecutors that Trump's campaign aides directly coordinated with people they believed were tied to the Russian government to collect damaging information on Clinton.

The legal barrage is a dramatic step forward in the investigation Trump frequently dismisses as a meritless fishing expedition – and a sign it will continue. Legal filings show that Mueller is also willing to dig back before the election into questionable activities by Trump aides as possible precursors to the activities during the campaign. Collecting such information is routine in presidential campaigns, but the involvement of a foreign government is remarkable.

Papadopolous's exchange with the professor came months before the anti-secrecy group WikiLeaks began releasing internal Democratic National Committee emails that cast an embarrassing light on Clinton's campaign. U.S. intelligence agencies concluded last year that the DNC's email was hacked at the direction of the Russian government.

Papadopolous was arrested in July, after he returned to the United States from a trip to Germany. But a judge agreed to keep the case secret until Monday after Mueller's office said that he had agreed to cooperate with investigators, and warned that revealing his arrest "could alert other subjects to the direction and status of the investigation."

Trump downplayed the charges Monday, and tried to point the finger at Clinton.

"Sorry, but this is years ago, before Paul Manafort was part of the Trump campaign," he tweeted. "But why aren't Crooked Hillary & the Dems the focus?????" He again insisted that his campaign had no cooperation with Russia, which the U.S. intelligence community has accused of using cyberattacks and fake news to influence the election in favor of Trump. "Also, there is NO COLLUSION!" he tweeted.

Sen. Mark Warner, the ranking Democrat and on Senate committee conducting its own investigation of Russian meddling called Manafort’s indictment “a significant and sobering step in what will be a complex and likely lengthy investigation.”

Other former Trump aides said they were unsure Monday what to make of the charges. Asked what the charges might mean for Mueller's broader inquiry, Michael Cohen, Trump's longtime personal attorney who has appeared before both the House and Senate intelligence committees, replied only "I really don't know." Carter Page, a Trump campaign foreign policy who has been interviewed by the FBI, said "this is not relevant to me."

Papadopolous was charged in July with making false statements to FBI agents and obstruction of justice. He pleaded guilty to making false statements on Oct. 5, but the case was not unsealed until Monday.

According to a court filing signed by prosecutors and Papadopolous, the former Trump aide met with a professor and a Russian woman in London in March 2016, after he joined the campaign. At the time, he mistakenly believed the woman was Russian President Vladimir Putin's niece. Papadopolous emailed an unnamed campaign supervisor to say he intended “to arrange a meeting between us and the Russian leadership to discuss U.S.-Russia ties under President Trump.” The filing does not name the professor or the Russian woman.

The supervisor responded that he would “work it through the campaign,” but would not make any commitments, according to the filing. It said Papadopoulos attended a “national security meeting” with Trump and other foreign policy advisors in Washington on March 31, 2016.

According to the filing, the professor told Papadopoulos in April 2016 that “the Russians had emails of Clinton” and “they have thousands of emails.”

WikiLeaks began publishing thousands of internal DNC emails in July of that year, as Democrats began to gather for their party's national convention.

After the London-based professor and a contact in the Russian Ministry of Foreign affairs expressed interest in a meeting with Trump, Papadopoulos in May 2016 sent an email to a high-ranking Trump campaign official with the subject line “Request from Russia to meet Mr. Trump,” according to the statement.

That email was forwarded to another campaign official with the message “Let[‘]s discuss. We need someone to communicate that DT is not doing these trips. It should be someone low level in the campaign so as not to send any signal.”

Papadopolous' lawyers declined to comment on the case.

Papadoplous was charged with misleading FBI agents about those exchanges when he met with them on Jan. 27. In court filings, Papadopolous admitted that he made false statements, including by telling agents that he was told about "dirt" on Clinton before he began working for Trump. In fact, he acknowledged, it occurred only later, and that the professor who offered him the information seemed "uninterested" until he told him that he had joined the campaign.

In a written plea agreement, Mueller's office said it would agree to recommend that Papadopolous face between zero and six months in prison.

RELATED: Manafort Gates Indictment Filed and Redacted

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The charges against Manafort and Gates include 12 counts of conspiracy, money laundering, failing to register as foreign agents and making false statements to investigators. Many of the charges are based on Manafort and Gates' work for the government of Ukraine, which began long before both men joined Trump's presidential campaign.

Manafort and Gates surrendered to FBI agents in Washington on Monday morning. They appeared briefly in federal court in the afternoon, where their lawyers pleaded not guilty on their behalf. Manafort, dressed in a dark suit, white shirt and blue tie, identified himself in court but said little else. Gates, wearing a dark suit and open-collar white shirt, did the same.

Both men surrendered their passports to the FBI and will be required to remain confined in their homes except for approved trips to consult with attorneys or receive medical treatment.

Mueller had been investigating Manafort, who resigned as Trump’s campaign chairman in August 2016, for his financial ties to a pro-Russia party in Ukraine.

The indictment makes no reference to Manafort's work on Trump's campaign. But it alleges that Manafort's efforts to conceal his work on behalf of Ukraine continued while he was running the campaign. As late as Aug. 19, 2016, three days before Trump fired him, the indictment alleges that Manafort and Gates sent "false talking points" to one of the political consulting firms they had hired to lobby on behalf of pro-Russian factions in Ukraine.

Rather, prosecutors allege that for more than a decade, Manafort and Gates worked secretly to influence the U.S. government on behalf of pro-Russian factions in Ukraine, then laundered their profits through a series of overseas businesses and bank accounts. In all, prosecutors alleged that $75 million passed through offshore bank accounts that the men controlled.

Manafort "used his hidden overseas wealth to enjoy a lavish lifestyle in the United States," prosecutors wrote. Investigators traced wire transfers from bank accounts in Cyprus that Manafort allegedly used to pay his landscapers and to buy a Mercedes and a Range Rover. Prosecutors also said that he used the accounts to pay more than $1.3 million to clothing stores in New York and Beverly Hills.

A spokesman for Manafort could not be reached to comment Monday morning.

Manafort has long been a central figure in Mueller's investigation. FBI agents raided his apartment over the summer. He has come under scrutiny both for his work in Ukraine and his participation in a meeting in 2016 between Donald Trump, Jr. and a Russian lawyer promising damaging information about Hillary Clinton.

According to the indictment, Manafort and Gates began working on behalf of Ukraine's pro-Russian government in 2006.

When U.S. authorities made inquiries about the payments last year, Manafort and Gates responded "with a series of false and misleading statements."

Gates had worked with Manafort in the private sector and followed him to Trump's campaign in 2016. Gates wound up moving to the Republican National Committee when Manafort was ousted from the campaign, and he helped set up a pro-Trump super PAC after the election.