Aides who came in with the former national security adviser are left trying to figure out whether they will follow their former boss and resign.
A trio of top staffers at the council, including acting-national security adviser Keith Kellogg, held an "all hands" meeting at the Eisenhower Executive Office Building Tuesday morning briefing the staff on the resignation and instructing them to go ahead with their jobs, an aide who attended told CNN.
Kellogg -- along with KT McFarland, Flynn's former deputy, and homeland security adviser Tom Bossert -- attempted to quell concerns around Flynn's resignation and job security at the national security body.
It was a tough sell: Many of those in attendance at the National Security Council stayed late into the night Monday to see how things shook out for their former boss and remain concerned that there could be wholesale changes after Flynn's departure.
Flynn, after misleading Vice President Mike Pence and other top White House staffers about his talks with the Russian ambassador, stepped down Monday night.
"I inadvertently briefed the vice president-elect and others with incomplete information regarding my phone calls with the Russian ambassador," Flynn wrote in his resignation letter.
Some of those National Security Council aides who were moving into office around the White House complex mere weeks ago feel stung by Flynn's departure. While not all considered themselves close to the retired US Army Lieutenant General, his departure does throw the national security organization -- the group tasked with implementing and coordinating the President's foreign policy and national security objectives -- into discord.
K.T. McFarland, Flynn's deputy, is at the center of these questions. Two White House officials said McFarland has not been asked to step down, but that in is unclear whether she will remain once a new national security adviser is named.
McFarland was seen walking into the West Wing on Tuesday morning.
A senior White House official said Monday that Trump was considering three names to replace Flynn: Retired Gen. David Petraeus, former Vice Admiral Bob Harward and retired Lt. Gen. Keith Kellogg, who is working as acting national security adviser.
Harward, a former Navy SEAL and the deputy commander of US Central Command under President Barack Obama, is the front-runner for the job, two White House official said.
But with new leadership comes new staff and the White House expects whomever they name will want to bring in their own people.
"When you have flag officers that come in, they tend to bring a cadre of their own people," said one official. "It doesn't mean there are guarantees of changes coming, but they do tend to bring in their own people."
The "all hands" meeting Tuesday morning was "upbeat," said the aide who attended, but realistic that there is considerable uncertainty in the National Security Council's current situation.
"There was an emphasis on the work that needed to get done, "the aide said. "They urged everyone that the mission of the council goes on."