WASHINGTON – If the first indictments handed down in special counsel Robert Mueller’s probe are any indication, things are looking increasingly bad for Michael Flynn.

Like former Trump campaign manager Paul Manafort, Donald Trump's first national security adviser failed for months to register as a foreign agent, in his case for his work for Turkey. And like former Trump foreign policy adviser George Papadopoulos, whose Oct. 5 guilty plea was unsealed Monday, Flynn allegedly lied to FBI agents about his contact with Russians.

The retired Army three-star general and former head of the Defense Intelligence Agency was fired after just 24 days in the job for misleading Vice President Mike Pence about conversations he had had with a Russian diplomat.

Mueller's rare leveling of a criminal charge for a violation of the Foreign Agent Registration Act against Manafort is a signal that it is in Flynn's best interests to work with the special counsel.

"Flynn is arguably responsible for the exact same kinds of crimes as Manafort — that is, acting on behalf of a foreign power and not registering,” said Neal Katyal, a former acting US solicitor general and a professor at Georgetown Law School. “One way of understanding the Manafort indictment is that Mueller is saying to Flynn, 'I haven’t indicted you yet, but you know you’re as guilty as Manafort is, you better start cooperating'."

Like Manafort, Flynn belatedly registered as a foreign agent after taking $530,000 from a Turkish businessman for work he did that Flynn acknowledged principally benefited the "Republic of Turkey." During the time he was doing that work, in the summer and fall of 2016, Flynn was serving as the Trump campaign's national security adviser.

While he was secretly being paid to represent Turkish interests, he sat in on classified intelligence briefings, advised Trump on national security issues, and wrote an opinion column supporting the extradition of a foe of President Tayyip Erdogan. Even after he was off Turkey’s payroll — and in the White House — he made some national security decisions that were in line with Erdogan’s interests.

Flynn registered as a foreign agent on March 7, three weeks after being fired and eight months after he signed on to lobby for Turkish interests. In that same filing, he disclosed that he secretly met in a New York hotel with Turkey's foreign minister, Mevlut Cavusoglu, and the country's energy minister, Berat Albayrak, who is Erdogan’s son-in-law.

Manafort and his associate Rick Gates are facing charges that they failed to register as agents for a foreign government under FARA, which requires that US citizens who lobby on behalf of foreign governments or political entities must disclose their work to the Justice Department within 10 days. However, as legal analysts and Manafort’s lawyer himself pointed out on Monday, prosecuting someone for a FARA filing is very rare. The US government has done so only six times since 1966, the last time the law was revised, and that has resulted in only one conviction.

The Justice Department has usually focused on “voluntary compliance” — registering late — rather than pursuing criminal charges, according to a 2016 audit of FARA enforcement by the Justice Department’s inspector general.

Mueller’s use of the FARA violation charge against Manafort and Gates may indicate that this is about to change, which legal experts say should worry Flynn.

Whatever happens with Flynn will also have different implications for the president.