As I wrote last week, that reflects poorly on Trump as a judge of character and as an employer, but it also allowed the president to distance himself from the investigation and point out that none of the charges against Manafort indicated collusion between the Trump campaign and Russia. (The Papadopoulos plea, though somewhat enigmatic, struck much closer to that matter.) As Trump made that point publicly, The Washington Post and Axios both reported that staffers inside the White House were relieved that Manafort had been charged, rather than Flynn.
The charges that Flynn seems most likely to face are similar to some that were brought against Manafort. Like Manafort, Flynn did not register under the Foreign Agent Registration Act at the time he did work for foreign governments, though like Manafort, he retroactively registered. Like Manafort, who is charged with making false statements, Flynn may have lied to the FBI. Flynn was pushed out of his job as national-security adviser on February 14, making him the shortest-tenured holder of that job in history, after the Post revealed that he had lied to Vice President Mike Pence and others about conversations he had with then-Russian Ambassador Sergey Kislyak. But the paper later reported that Flynn had also lied to the FBI about those conversations.
There are also other counts on which Flynn might be in trouble: His conversations with Kislyak could violate a law that prevents private citizens from conducting foreign policy, though it has never successfully been used to prosecute an American, and many analysts doubt it will be here. There is scrutiny of Flynn’s work for Turkey, for which he retroactively filed under FARA, including an alleged scheme to kick Fethullah Gulen, a cleric and enemy of Turkish President Recep Tayyip Erdogan out of the country. Members of Congress have focused on trips he made overseas, including one to celebrate the anniversary of the Kremlin propaganda network RT. As a former top general, Flynn was required to seek permission to be paid for those trips, and he also stands accused of not disclosing them when seeking renewed security clearance. Flynn was also involved in a bizarre Middle Eastern civil-nuclear scheme.
Whatever the superficial similarities between the Manafort and Flynn situations, though, the key difference is that a Flynn indictment would put the Mueller probe in the White House. Manafort was pushed out of the campaign in August and never worked in the Trump administration (though he is said to have remained in contact with Trump for months). Flynn, however, worked in the White House for almost a month. That means he could have discussed many of the potential areas for charges—from conversations with Kislyak to Gulen to who knows what—with any number of White House staffers on any level. Mueller could call them in for questioning. Even if none of those staffers did anything illegal, and at this point there’s no indication they did, the threat of testimony will create new stress and distraction in a White House already riven with both. They’ll also all need lawyers, and good expensive ones; the Papadopoulos plea-deal is a vivid illustration of the dangers of talking to federal agents. (Trump has offered to contribute $430,000 to legal fees, but the more staffers involved, the faster that will be used up.)