'If you go after the intel community, they'll go after you': Morning Joe explains how Sally Yates took out Flynn

MSNBC's Mika Brzezinski has been predicting that Michael Flynn, who resigned late Monday as national security advisor, would be the first top official to leave the Trump administration.

She and "Morning Joe" co-host Joe Scarborough expressed concerns about Flynn throughout the White House transition -- and they said his departure raises even more questions about the president's relationship with Russia.

"We have been warning this president and Gen. Flynn on the air for months that (if) you go after the intel community, the intel community will go after you," Scarborough said. "They are the last people you want to go after."

Former acting attorney general Sally Yates warned the White House counsel that Flynn may have been blackmailed by Russia, Scarborough said, but the White House insisted up to this week that the national security advisor had the president's full confidence.

"Who knew in the White House, and when did they know in the White House and why was the vice president of the United States kept in the dark and allowed to go on television and lie?" Scarborough asked. "The only reason we're finding out about (Flynn's conversations with the Russian ambassador) now is because a patriot did leak this."

According to published reports, Flynn told Vice President Mike Pence he had not discussed sanctions with the Russian ambassador before the Obama administration ended -- but Scarborough finds it difficult to believe that no one else knew about those conversations.

"Was Mike Pence the only one who didn't know in the White House that was kept in the dark?" Scarborough said. "Because we certainly know that the White House counsel had to know. You've got to believe the president of the United States had to know. Certainly the Justice Department knew, and if the acting attorney general knew -- did (Jeff) Sessions know? There has to be a very long list of people in the White House who kept the vice president of the United States in the dark, allowed him to lie on national television and then not correct it afterwards."

Brzezinski said the wide-ranging episode raises the central question swirling around the Trump administration.

"What is the relationship with Russia?" she said. "There is something -- it's not nothing anymore. It's not (a) mistake, it's not being newbies -- you know, this isn't Nordstrom, and just ethically inappropriate. This is troubling on a deep, global level."