The president posted a video last Friday of her speech to the California chapter of CAIR - the Council on American-Islamic Relations which was founded in 1994. Omar also said Muslims had "lived with the discomfort of being a second-class citizen and, frankly, I'm exhausted of it, and every single Muslim in this country should be exhausted of it".
In her address, Omar had said the CAIR "was founded after 9/11 because they recognized that some people did something, and that all of us were starting to lose access to our civil liberties".
But her stay has coincided with an ugly war of words that has pitted Trump against the new breed of Democrats like Ocasio-Cortez and Ilhan Omar.
The Minnesota congresswoman said on Sunday evening that she had experienced "an increase in direct threats on my life - many directly referencing or replying to the president's video". "It has to stop".
But "what we are saying is, to have a message that appeals to people in a way that does not menace them", she said. She tweeted back at Kilmeade and Crenshaw: "This is unsafe incitement, given the death threats I face".
House Speaker Nancy Pelosi took time out from an official trip to issue a strong statement urging Trump to remove the clip featuring Minnesota congresswoman Ilhan Omar.
She followed standard USA diplomatic protocol of senior officials not criticising the president while overseas.
Omar said in a statementposted on Twitter Sunday that numerous increased threats she had received were "directly referencing or replying to the President's video".
Over the weekend, after Trump had entered the equation, Bernie Sanders and Elizabeth Warren, both presidential candidates on the left of the Democratic party, came out in defence of Omar. She referenced the 9/11 attacks, somewhat dismissively, with the phrase "some people did something".
Members of the Congressional Black Caucus said in a conference call Monday they are concerned for Omar's safety, especially as Trump campaigned in Minnesota. "I thank Capitol Police, the Federal Bureau of Investigation, the House Sergeant at Arms, and the Speaker of the House for their attention to these threats".
Fox News Channel host Brian Kilmeade said on a "Fox & Friends" segment on Omar, "You have to wonder if she's an American first". And now, the president has accused her of trivialising 9/11.
"This is endangering lives", she said, accusing Mr Trump of fomenting right-wing extremism. "If she continues to do it, the president will continue to call her out, call her out by name, and he's not going to be ashamed, nor should he be".
She rocketed to global celebrity as an inspiration for women after the unexpected election win, and she became only the second leader to give birth while in office since Pakistan's Benazir Bhutto. Ultimately, it should not matter how adamantly Trump disagrees with Omar.
But she made explicitly clear that new Congresswoman Alexandria Ocasio-Cortez - an emerging force in United States politics who is often simply referred to as AOC - and fellow young progressives elected in 2018 represented only the margins of American society.
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