Men in Black, Dogma and later career
Fiorentino played the female lead, Dr. Laurel Weaver, in the 1997 film Men in Black, for which she was nominated for a Blockbuster Entertainment's Award for Favorite Supporting Actress in Science Fiction. She appeared alongside Ving Rhames, John Leguizamo and David Caruso in the 1998 direct-to-video film Body Count, which Variety called "an after-the-heist road movie that sizzles here and there but ends up going no place special." In 1999, she starred in Dogma as abortion clinic employee Bethany Sloane who is tasked with saving the world.
In years following, it was rumored Fiorentino did not get along with Dogma director Kevin Smith, which generated negative press for her. In an interview with TV Guide in 2000, Smith stated, "Linda created crisis and trauma and anguish. She created drama while we were making a comedy. She was ticked off that there were other people in the movie who were more famous than she was." He also accused Fiorentino of avoiding promotional duties after "going nuts" at the film's poster, which had spliced her head onto another woman's body and amplified her cleavage. "She never did a photo shoot," Smith said. "It's not like we were hinging on all that Fiorentino press – I fought to cast the woman in the movie."
However, in 2018, Smith stated that rumors of a falling out between the two had been misconstrued and overstated, and that while the two had not spoken in years, they amicably reconnected following his near-fatal heart attack. Blaming himself, Smith attributed the rumors to a remark he had made on the film's commentary track, which had later been sensationalized: I remember on a commentary track on the DVD — Janeane Garofalo was in the movie and at one point I said it would have been better if she played the lead, which was a really shitty and stupid thing to say. Thoughtless, considering that Linda was the lead and Linda did a great job. So, it had been years since I had spoken with Linda and I got an email from her. And of course, I was thankful to hear from her and it also gave me a chance to say I'm so sorry that I ever said that thing years ago. It gives you a chance to make amends. So that was my favorite one. I heard from so many people, but that one really stood out for me because, if somebody had said, 'Oh, the movie would have been better if [co-star] Ben Affleck directed it,' that would have hurt my feelings. I know it hurt her feelings and really unnecessarily because I always loved her performance in the movie.After a co-starring role with Paul Newman in the 2000 heist film Where the Money Is, and a lead role in the 2002 film Liberty Stands Still, Fiorentino's career slowed to a halt. She was in talks to star in a series being prepared by Tom Fontana, but did not take the project. Fiorentino was attached to a Georgia O'Keeffe biographical drama called Till the End of Time, but the project stalled when Fiorentino had a falling out with German producer Karel Dirka regarding provocative sex scenes. "You have rights, as an artist and as a woman," she said. "It's not as if I didn't agree to do some nudity. But they crossed the line. It was a question of integrity."
Fiorentino's character was written out of Men in Black II (2002) to accommodate the return of Tommy Lee Jones as the co-lead of the film and partner to Will Smith's character. According to producer Laurie MacDonald, "It turned out not to be a big enough role. We would have loved to have her, but when we began to develop the story, we couldn't find a [major] place for her. We always knew that the movie would be about bringing Tommy Lee Jones back." Kristin Lopez, writing an expose for RogerEbert.com titled "Hollywood's Difficult Women," brought up rumors that Jones' return was, in fact, contingent upon Fiorentino's absence and that the studio responded to this stipulation accordingly.
In 2007, Fiorentino optioned the rights to a screenplay about Russian poet Anna Akhmatova with plans to produce and to possibly star in and direct, but the project was dropped. During this period, she was reported to be developing two documentaries, neither of which moved forward. Fiorentino's most recent screen role was a supporting character in Once More with Feeling, released direct-to-video in 2009.