1990–2008: Mature roles and Broadway debut
Plimpton appeared in the Robert De Niro-Jane Fonda 1990 romantic drama Stanley & Iris in a supporting role. She also appeared in the 1991 TV movie A Woman At War in the lead role as Helene Moszkiewiez. Plimpton played the starring role of Samantha in the film Samantha (1991). She appeared as an activist in the independent film Inside Monkey Zetterland released in 1993. Plimpton appeared in the television film Daybreak (1993, HBO). She appeared in the Showtime television film Chantilly Lace. Plimpton had a featured role in the film Josh and S.A.M. (1993) as a runaway who takes care of the two boys. She played the lead in The Beans of Egypt, Maine, based on the Carolyn Chute novel. Plimpton also appeared as herself in the independent film by Eric Schaeffer My Life's in Turnaround (1993), a movie about filmmakers trying to make a movie. She appeared as a close friend of radical feminist Valerie Solanas in the film I Shot Andy Warhol (1996).
In 1997, the Showtime Network cast Plimpton as the female lead in a television film, The Defenders: Payback. Two more episodes (The Defenders: Choice of Evils and The Defenders: Taking the First) were aired in 1998. This show was a retooling of the classic television show by the same name, and the characters were descendants of Lawrence Preston, a role reprised by actor E. G. Marshall. Plimpton played the granddaughter, M.J. Preston. The intent was to spin the program off as a series, but Marshall died in 1998. The decision was made to not continue production due to Marshall's death. Plimpton became involved with the Steppenwolf Theatre Company in Chicago, appearing in Hedda Gabler (2001) among others. She appeared in the John Waters film Pecker in 1998. The film received mixed reviews—for example, the SF Gate reviewer wrote, "...Waters' patented brand of off-color fun is watered down", but wrote that Plimpton's work was "solid". The 1999 film 200 Cigarettes received generally negative reviews, but the AllMovie reviewer wrote of Plimpton: "...woefully underappreciated Martha Plimpton gets laughs as a bundle of neuroses who grows more and more stressed out as people fail to appear for her party..." In 1999, Plimpton had a recurring role in the sixth season of the NBC medical drama ER as Meg Corwyn.
In 2001, Plimpton starred in The Sleepy Time Gal. In 2002, she appeared in the documentary Searching for Debra Winger and was nominated for a Primetime Emmy Award for her guest appearance on the television drama Law & Order: Special Victims Unit. Plimpton was the voice of Miss Crumbles in the 2004 animated film Hair High by Bill Plympton. In 2004, she guest-starred in an episode of 7th Heaven. Plimpton wrote the episode of the show entitled "Red Socks", which aired in 2005. She had a recurring role in the NBC show Surface (2005–06). From October 2006 to May 2007, Plimpton was in the stage play The Coast of Utopia, a trilogy of plays by Tom Stoppard at Lincoln Center. She won a Drama Desk Award and was nominated for a Tony Award for Featured Actress in a Play. From August to September 2007, Plimpton appeared in A Midsummer Night's Dream in the Public Theater Shakespeare in the Park production as "Helena".
Plimpton co-founded a production company, Everything is Horrible, which has produced short films for the Internet. She received her second nomination for a Tony Award in 2008, Best Performance by a Featured Actress In a Play, for her work in Top Girls at the Biltmore Theater. In November 2008, Plimpton earned a positive review from Ben Brantley in The New York Times for her role as Gladys Bumps in the Roundabout Theatre Company production of Pal Joey on Broadway: "...the ever-daring Ms. Plimpton exudes a been-there, frowzy sensuality that summons a host of hard-bitten dames from 1930s movie melodramas. Leading the nightclub act 'That Terrific Rainbow,' she has the period style down pat and a more than passable voice." Plimpton received her third consecutive Tony nomination, for Best Featured Actress in a Musical. She appeared in the 2008 Entertainment Weekly photo issue spread as one of "The Hardest Working Actors In Showbiz". Plimpton said in the write-up, "I went to jury duty the other day, and somebody said, 'You always play drug addicts!' I've played a few on TV, and I imagine because the shows get replayed, it seems like more. But yeah, people tend to see me as this pregnant teenage heroin addict." In 2008, Plimpton performed a duet with singer Lucy Wainwright Roche on Roche's EP 8 More, singing the Bruce Springsteen song "Hungry Heart". The two had performed the song in 2008 at Joe's Pub and later in 2008 at the Zipper Factory. In 2009, Plimpton was profiled by The New York Times for their "A Night Out With..." series, in which Plimpton hosted an evening of poker at The Players.