Sigcho-Lopez is chair of the Committee on Housing and Real Estate and alderman for the 25th Ward.
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A resolution to remove him failed 29 to 16 Monday afternoon.
During the meeting, Sigcho-Lopez did not apologize for taking part in an anti-war rally, where an American flag was burned last month.
However, he did say during the meeting that he will "take accountability."
There were some heated outbursts during the meeting, which was called by several aldermen who wanted Sigcho-Lopez removed as chair after the rally.
"I told him that, as an alderman, as a person that's elected to represent veterans and the residents that have lost their loved ones in the military, that he hasn't learned to balance activism and politics to a point where he's effective in both," Alderman Chris Taliaferro previously said.
Sigcho-Lopez said "by no means" will he condemn a veteran for using his First Amendment rights.
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He previously said he arrived at the rally after the flag burning, and wasn't aware it had happened. However, the ashes of the flag were at his feet.
He said he and his family have received death threats in recent days.
"This was a political stunt. Nevertheless, I do think that this is an important step to recommit our Council to make sure that we, as a Council, are discussing the priorities of Chicagoans," Sigcho-Lopez said.
The aldermen who introduced the resolution said they support free speech rights, but City Council leaders need to be held to a higher standard.
"Legitimizing the extremism by a leader in this body is dangerous, and sends the wrong message to our residents. That's why we're asking for accountability," 36th Ward Ald. Gilbert Villegas said.
"Now, Alderman Sigcho-Lopez has a right to be inflammatory, but he has a bigger responsibility as a leader in this body and a leader in this city," 34th Ward Ald. William Conway said.
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Mayor Brandon Johnson defended Sigcho-Lopez last week.
In a statement Monday, he said: "I believe strongly in the democratic process and was pleased to see Ald. Sigcho-Lopez and Ald. Taliaferro reaching a mutual understanding and moving forward. I once again applaud members of City Council for their thoughtful debate and look forward to continuing to work collaboratively to address the urgent needs of all Chicagoans."
Some members of the public had to be shown the door Monday.
Before the meeting, a group of anti-war protesters staged another flag burning in front of City Hall, and also spoke in support of Sigcho-Lopez, who did not attend that rally.
Before Monday's vote, debate among aldermen was quite civil, and many expressed a desire to move on from this controversy.