MacLachlan brought his somewhat stilted persona to the small screen for Lynch's fleeting and cultish TV series, "Twin Peaks" (ABC, 1990-91). As Special Agent Dale Cooper, the eager beaver, super-efficient FBI man with a weakness for non sequiturs, cherry pie and a "damn fine cup of coffee", he blossomed as an actor, his former stiffness becoming stylish and engagingly goofy. In a show full of weird characters and strange happenings, Cooper provided a likable and reassuring anchor. MacLachlan's dramatic transformation was less surprising for those lucky few who had seen his portrayal of a friendly alien in "The Hidden" (1987), a much underrated sci-fi action movie which could be viewed as a dry run for his splendid "Twin Peaks" work.
MacLachlan put his childhood piano and vocal lessons to good use in the thankless reactive role of keyboardist Ray Manzarek in Oliver Stone's mishmash Jim Morrison biopic, "The Doors" (1991). He reprised his role as the dream-obsessed Cooper with an extended cameo in the pull-out-the-stops prequel "Twin Peaks: Fire Walk With Me" (1992) before taking small parts in the dramas "Where the Day Takes You" (1992) and "Rich in Love" (1993). Though he has generally made a strong impression in stylized genre fare, MacLachlan did not quite work as the enigmatic, tormented Joseph K in a feature adaptation of Franz Kafka's "The Trial" (1993).
He next decided to take a vacation from his dark side in "The Flintstones" (1994) and his villainous Stone Age yuppie fit perfectly with the film's cartoonish goings-on. The disastrous "Showgirls" (1995) reintroduced him to the world of the BOMB and replaced "Dune" as the worst movie he had ever made, although he still believed that honor should go to "Don't Tell Her It's Me" (1990), a little bit of nothing starring Steve Guttenberg. Rebounding, he found fertile ground in David Koepp's quirky tip of the hat to Rod Serling, "The Trigger Effect" (1996). Koepp's compelling narrative provided MacLachlan with his best vehicle since "Twin Peaks" and made this small movie worthy of the big time. He also earned strong notices for his work as Nastassja Kinski's opinionated husband in Mike Figgis' "One Night Stand" (1997).
MacLachlan turned in some of his best work of the 90s for the small screen. As a naive, rookie prison guard taken hostage in HBO's "Against the Wall" (1994), he provided the acclaimed docudrama with its point-of-view, helping John Frankenheimer earn the first of four directing Emmys he would receive over a five-year period. That year's "Roswell" (Showtime) returned him to an almost Lynchian world of aliens as an old army pro fighting to regain the respect lost when the little green men first landed, while the NBC pilot remake of "The Conversation" (1995) offered the choice role originated by Gene Hackman in the 1974 original. A hard-driving, bootleg whiskey-deliverin' Tennessee boy in stunt coordinator Andy Armstrong's impressive writing-directing debut "Moonshine Highway" (1996), he got to fulfill his James Bond fantasies as Sean Dillon, an Irish terrorist turned British spy, in two 1996 Canadian movies airing on TMC in 1998, "Jack Higgins' Thunder Point" and "Jack Higgins' The Windsor Protocol.”
Returning to features, MacLachlan offered a featured performance as a slick Hollywood agent in Figgis' "Time Code" (2000) but his work took a back seat to the director's experimental use of four digital cameras capturing the action in four different places simultaneously. He made quite an impression in Michael Almereyda's Gen-X "Hamlet" (also 2000) cast as Claudius, a lusty, brilliant corporate smoothie who in this rendition has usurped his "throne" from older brother Sam Shepard and coupled with Hamlet's (Ethan Hawke) mother (Diane Venora) as the Bard would say "before the funeral baked meats were cold." That fall also marked his return to series work as a recurring love interest for Kristin Davis' Charlotte in a seven-episode run on the popular HBO sitcom "Sex and the City". The couple met in dramatic fashion with his yuppie surgeon enjoying a Prince Charming moment by coming to Charlotte's rescue when she nearly gets hit by a cab.
In “The Spring” (NBC, 2000), MacLachlan played a widowed father who takes his son (Joseph Cross) on a camping trip, but stumbles upon a small isolated town hiding a fountain of youth that has kept its residents, including the township’s doctor (Alison Eastwood), forever young. After a supporting role in the sci-fi thriller “Xchange” (HBO, 2001), MacLachlan played a college lit professor who develops a bond over literature that turns into an affair with one of his students (Michelle Williams) in “Me Without You” (2001), a coming-of-age drama spanning three decades about the gradual separation of two life-long friends (Williams and Anna Friel). He made a brief appearance in the straight-to-video released “Perfume” (2002), an improvised ensemble parody of the fashion world, then had a small role in the Polish Brothers’ hallucinatory fairy tale, “Northfork” (2003). In “Miranda” (2003), he played a sleek millionaire with a kinky obsession for an elusive and enigmatic confidence woman (Christina Ricci) who has captured the amorous attention of a mild-mannered librarian (John Simm).
Maintaining a consistent presence on cable television, MacLachlan next appeared in “The Librarian: Quest for the Spear” (TNT, 2004), playing an evil ex-librarian and head of the dastardly Serpent Brotherhood who seek to reconnect the three pieces of the Spear of Destiny so they can rule the world. Standing in their way is a meek and mild student (Noah Wylie) working at the New York Public Library where the pieces are housed. He next portrayed the spirit of Cary Grant in “Touch of Pink” (2004), a romantic comedy about a young gay Asian-Canadian man in London who has a charming English boyfriend, an unsuspecting mother and an active fantasy life with the Hollywood legend. MacLachlan returned to television with an episode of “Law & Order: Special Victims Unit” (NBC, 1999-2006), then got his own one-hour drama series, “In Justice” (ABC, 2005- ), playing an ambitious and egotistical lawyer who leads a team of passionate lawyers assisting the wrongly accused by reopening their cases in an attempt to prove their innocence. Meanwhile, MacLachlan was set to be seen in “Mysterious Island” (Hallmark Channel, 2006) as a daring Civil War captain who helps his fellow soldiers escape a Confederate prison via hot air balloon only to crash land on a remote island populated with pirates, mutant monsters and an eccentric Nemo-like scientist.