Last night on The Kelly File, we told you about Brandeis University’s decision to revoke an honorary degree for Ayaan Hirsi Ali, a women’s rights advocate in the Muslim community.

WATCH: Megyn Talks to Islam Critic, Takes on CAIR Member

Hirsi Ali, a Somali-born woman and United States citizen, was subjected to genital mutilation and forced to flee her marriage. She has endured death threats for speaking out against Islam. Recently, she executive produced and starred in a documentary called, "Honor Diaries."

Last night, Megyn Kelly spoke to Hirsi Ali and also took on Ibrahim Hooper, from the Council on American-Islamic Relations. That group was behind the movement to push Brandeis to take back Ali’s honor.

During part two of the interview, above, Megyn questioned CAIR’s tactics for attacking some of its critics.

Democratic Senator Chuck Schumer (N.Y.) has previously stated, “[CAIR] we know has ties to terrorism… prominent members of [CAIR’s] current leadership… also have intimate connections with Hamas.”

Hooper called the Kelly File interview a “smear campaign” to which Megyn replied, “You can come on and denounce hateful bigotry, but it can never be said against you because that also is hateful bigotry.”

Referring to CAIR as a civil rights organization, Hooper challenged, “The most public Muslim organization in the nation, please find something that CAIR has done or said in those 20 years that you find either extreme, objectionable, intolerant, whatever.”

He continued, “Every day we’re defending the Constitution from people like Hirsi Ali who would change the Constitution so that Muslims wouldn’t have civil rights.”

Megyn took the challenge, citing the group’s defense of PIJ, a terrorist group that killed over 100 people.

Hooper shot back, “When you do your oppositional research, it might be helpful to go to someplace other than Internet hate sites.”

The pair went back-and-forth about the First Amendment, with Megyn pointing out that it allows for both good and bad speech.

“Your problem is you don’t want to respond, you want to silence,” Megyn said.

Watch the full interview above, and check out Part One here.