What she did at the end of the song shocked viewers: She held up a picture of Pope John Paul II and ripped it in two.
Eighteen years later, amid continuing revelations of sexual abuse in the Catholic Church, O'Connor's anger is matched by the public worldwide. A Facebook page has even been started called "Apologize to Sinead O'Connor NOW."
O'Connor spoke recently with NPR's Guy Raz about ripping up the photo and how she feels about the church today.
"I'm an intelligent woman. I knew how people would react," she says. "I considered myself a spiritually, intellectually developed woman. ... I was perfectly willing to deal with the consequences, the main one of which was people saying I'm a nutcase, which I agree with anyway."
O'Connor says she wasn't looking to be vindicated.
"It's more important to realize that they [the victims] have been vindicated and believed and treated with respect after struggling for, some of them, nearly 40 years, literally, to be recognized," she says.
In spite of her objections to the church's handling of abuse, she says she loves the institution.
"A lot of people misinterpret me and think I'm somehow anti-Catholic, and I'm not," she says. "I've acted out of a passionate love of the Holy Spirit and what is good about Catholicism. ... I have nothing but respect for any priest and nun that I've ever met. ... They've been disrespected and misrepresented. I think there's so much that's beautiful about Catholicism, but that has been clouded by the cover-up more even than the abuse."
She questions the beliefs of those in the church who would hide abuse: "[It's] as if they don't believe in God. They certainly don't believe in a God that is watching them or what they're doing."
O'Connor says new leadership is needed in the Catholic Church and supports democratic elections for the pope. She says she feels the flurry of abuse revelations over the past few years is just evidence that the Holy Spirit is "doing some serious housekeeping" and exposing the lies.
But she's still hopeful about the future of the institution: "We don't want to throw the baby out with the bath water. There's something beautiful there."
SIC: NPR