NEW YORK, NY - NOVEMBER 17: Retired Lt. Gen. Michael Flynn (C) arrives at Trump Tower, November 17, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and high level positions for the new administration. (Photo by Drew Angerer/Getty Images)
PHOTO: Drew Angerer/Getty Images
NEW YORK, NY - NOVEMBER 17: Retired Lt. Gen. Michael Flynn (C) arrives at Trump Tower, November 17, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and high level positions for the new administration. (Photo by Drew Angerer/Getty Images)
Now playing
02:54
NYT: Trump team knew about Flynn investigation
PHOTO: Getty Images
Now playing
02:07
Trump to declassify documents in Russia probe
PHOTO: CNN
Now playing
02:04
Starr: Mueller is getting closer to the truth
PHOTO: CNN
Now playing
02:35
Giuliani: Trump, Comey never discussed Flynn
PHOTO: Getty Images
Now playing
01:24
Trump calls on Sessions to end Mueller probe
Now playing
01:10
Giuliani: Not sure colluding is a crime
conspiracy collusion explainer orig mg_00005015.jpg
PHOTO: Shutterstock
conspiracy collusion explainer orig mg_00005015.jpg
Now playing
01:01
Difference between conspiracy and collusion
PHOTO: Fox News Channel
Now playing
02:57
Putin denies Russia interfered in US election
PHOTO: McNamee/Dunham/Getty Images
Now playing
01:50
Trump deflects question over Russia indictments
WASHINGTON, DC - JUNE 21:  Special counsel Robert Mueller (2nd L) leaves after a closed meeting with members of the Senate Judiciary Committee June 21, 2017 at the Capitol in Washington, DC. The committee meets with Mueller to discuss the firing of former FBI Director James Comey.  (Photo by Alex Wong/Getty Images)
PHOTO: Alex Wong/Getty Images
WASHINGTON, DC - JUNE 21: Special counsel Robert Mueller (2nd L) leaves after a closed meeting with members of the Senate Judiciary Committee June 21, 2017 at the Capitol in Washington, DC. The committee meets with Mueller to discuss the firing of former FBI Director James Comey. (Photo by Alex Wong/Getty Images)
Now playing
00:58
Podesta mocks Trump: Mueller caught the witches
PHOTO: CNN
Now playing
01:54
Stone: Think I'm probably person in indictment
dana bash reax
PHOTO: CNN
dana bash reax
Now playing
01:36
Bash on DNC hacking: This is a major crime
PHOTO: Pool
Now playing
02:34
Rosenstein: Think as Americans, not partisans
Now playing
01:39
Dem: Strzok hearing was about political theater
US President Donald Trump (L) chats with Russia's President Vladimir Putin as they attend the APEC Economic Leaders' Meeting, part of the Asia-Pacific Economic Cooperation (APEC) leaders' summit in the central Vietnamese city of Danang on November 11, 2017. / AFP PHOTO / SPUTNIK / Mikhail KLIMENTYEV        (Photo credit should read MIKHAIL KLIMENTYEV/AFP/Getty Images)
PHOTO: MIKHAIL KLIMENTYEV/AFP/Getty Images
US President Donald Trump (L) chats with Russia's President Vladimir Putin as they attend the APEC Economic Leaders' Meeting, part of the Asia-Pacific Economic Cooperation (APEC) leaders' summit in the central Vietnamese city of Danang on November 11, 2017. / AFP PHOTO / SPUTNIK / Mikhail KLIMENTYEV (Photo credit should read MIKHAIL KLIMENTYEV/AFP/Getty Images)
Now playing
02:49
Senate panel agrees Putin tried to help Trump
trey gowdy
trey gowdy
Now playing
02:03
Gowdy on Russia investigation: Finish the hell up
(CNN) —  

Michael Flynn told Donald Trump’s transition team that he was under federal investigation for secretly working for Turkey, according to a report Thursday in the New York Times. Trump went ahead and hired Flynn as his national security adviser anyway.

Wrote Timesmen Matthew Rosenberg and Mark Mazzetti:

“Mr. Flynn’s disclosure, on Jan. 4, was first made to the transition team’s chief lawyer, Donald F. McGahn II, who is now the White House counsel. That conversation, and another one two days later between Mr. Flynn’s lawyer and transition lawyers, shows that the Trump team knew about the investigation of Mr. Flynn far earlier than has been previously reported.”

That wasn’t the first time that Trump had been warned regarding Flynn. In fact, two days after his election, Trump traveled to Washington to meet with then-President Barack Obama – a meeting in which Obama cautioned Trump away from naming Flynn as his national security adviser. “Given the importance of the job, the President thought there were better people for it, and that Flynn wasn’t up for the job,” a former senior Obama administration official told CNN of Obama’s decision to ward Trump off of Flynn.

And, it wasn’t the last time Trump was warned about Flynn either. On January 26, acting Attorney General Sally Yates met with McGahn, making clear that, based on what the Justice Department had seen, Flynn had been compromised by the Russians and was a potential blackmail target.

It took Trump 18 days after that Yates-McGahn meeting to fire Flynn. And when he did so, it was because Flynn had misled Vice President Mike Pence about the nature of his conversations with Russian ambassador Sergey Kislyak, not because of any of the warnings Trump had been given before and during his presidency.

Despite all of the trouble Flynn caused him, Trump continued to defend Flynn in public and private. In fact, Trump may have ensured the appointment of a special counsel to oversee the Russian investigation when he reportedly met with James Comey on Feb. 14 and urged the then-FBI Director to find a way to drop the probe into Flynn’s ties to the Russians.

Why? Why would Trump name as his top national security adviser a man he knew was under federal investigation, a man he had been warned against by a sitting president of the United States? And then why would he keep Flynn in that job even after it was made clear to Trump that Flynn was lying about his contacts with the Russians and was vulnerable to being blackmailed by that country?

On its face, it makes zero sense. Trump hates when his subordinates make bad news for him. And he is quick to blame others for problems within his administration. So, what makes Flynn different?

Two things – I think.

First, Flynn is a retired general. Trump loves to surround himself with military men and revels in his role as commander-in-chief. (It also probably didn’t hurt that Flynn had been fired by Trump nemesis Obama.) If Trump defers to anyone, it’s generals. That deference likely gave Flynn a far wider berth than the average staffer bringing bad news down on Trump.

Second, Flynn was one of the earliest and most outspoken supporters of Trump. Trump is someone who prizes loyalty above all else. And Flynn was there almost from the very beginning – blasting the Republican establishment, leading the “lock her up” chants against Hillary Clinton and, generally speaking, doing whatever was asked of him by Trump. Trump liked that loyalty. And he wanted to reward Flynn for it. Everything else paled in comparison to that.

Prioritizing loyalty and military service is, of course, Trump’s right. But for someone who premised a campaign – and a presidency – on his unblinking ability to not only pick the best and brightest but then to find ways to make them even more successful, Trump’s misjudgment of Flynn seems like a major black mark.

His continued defense of Flynn – well past the point of loyalty or even reason – is even more baffling. Flynn is the origin – or at least an origin – of many of the major problems that threaten Trump’s presidency. Everyone sees that. Everyone, it seems, except Trump.