Whitaker played a kindly plastic surgeon in "Johnny Handsome" (1989), and the actor's heavy-lidded, unhurried delivery suggested the naiveté of his Mama's Boy character in "A Rage in Harlem" (1991) and the skeptical intelligence of his insurance investigator in "Consenting Adults" (1992). All three projects showed how easily he could rise above otherwise bland material. He displayed a mesmerizing depth in "Diary of a Hitman" (1991, released in the USA in 1992), the feature directing debut of acting coach Roy London. Hired to knock off the wife and child of a born-again commodities broker who claims his wife is a drug addict and the infant crack baby not his, Whitaker goes about saving the intended victim (and himself) when he discovers the broker lied in this modest, expertly-acted indie. He was also quietly, irresistibly sympathetic as a British soldier kidnapped by the IRA in Neil Jordan's highly praised "The Crying Game" (1992).

The unexpected commercial success of that film led to increased interest in Whitaker's long-form directorial debut (he had previously directed music videos), "Strapped" (HBO, 1993). Filmed on location in Brooklyn's notorious Fort Greene district, the gritty urban drama screened at various international film festivals and earned the director's award for best first feature in Toronto. Deluged with offers to direct, Whitaker remained a familiar face on screen while pondering his filmmaking future, segueing effortlessly from Hollywood genre fare, both big-budget ("Blown Away" 1994; "Species" 1995) and small ("Body Snatchers" 1993). His ability to evoke audience empathy continued undiminished as he affectingly portrayed physically and mentally maimed fathers in "Jason's Lyric" (1994) and "Smoke" (1995). Admirably unafraid to play gay characters, Whitaker also fared well as a down-to-earth designer in Robert Altman's misfired satire, "Ready to Wear (Pret-a-Porter),” and returned to the world of jazz as trumpeter Buddy Chester, stricken with a fatal brain tumor in Showtime's "Lush Life" (both 1994).

Whitaker chose to make his feature directing debut with "Waiting to Exhale" (1995), the Black female ensemble drama adapted from Terry McMillan's best seller. Boasting a large cast headlined by Whitney Houston and Angela Bassett, the film opened to mixed reviews—mostly complaints about the episodic nature of the story—and healthy box office. He returned to the other side of the camera as John Travolta's best friend in "Phenomenon" (1996) but was back in the director's chair for "Hope Floats" (1998), unable to keep the leaky craft starring Sandra Bullock from sinking. Though similar to "Waiting to Exhale" in its story of a character trying to regain belief in herself, Whitaker's sophomore effort was far less compelling, and Bullock (who also executive produced) had very little help from her mostly muted and wooden fellow actors. Although he admittedly prefers directing to acting, the demand for him to do the latter has kept him primarily in front of the camera since "Hope Floats,” though he did executive produce and helm a busted ABC pilot "Black Jaq" in 1998.

Whitaker's school security guard ("a $5 cop with a $50 attitude") ends up a hostage in "Light It Up" (1999), a thoughtful, if too-often predictable teen drama. He also played a Federal Marshal who gets his kicks watching low-lifes squirm in that year's "Witness Protection" (HBO). He then stepped back into the shoes of a hit man as the titular character of Jim Jarmusch's whimsical "Ghost Dog: The Way of the Samurai" (1999), imparting a dignified gravity to the character's meticulously ordered existence defined and regulated by an 18th-century text, "Hagakure: The Book of the Samurai". Whitaker's complete immersion in and dead-on rendering of Jarmusch's anachronistic antihero, coupled with The RZA's high-voltage, hip-hop score, went a long way toward making what is arguably Jarmusch's most accessible film his most commercial one.

He reunited with producer-star Travolta as evil dominators of the remnants of mankind in the notoriously awful sci-fi opus "Battlefield Earth: The Saga of the Year 3000" (2000), adapted from the novel by Scientology founder L. Ron Hubbard. Following a supporting turn in Vietnamese refugee tale "The Green Dragon" (2001) and a stint as Daguerreotypist Picard in the CBS television miniseries "Feast of All Saints" (2001) based on the Anne Rice horror novel, Whitaker made a believably reluctant villain as part of the team of home invaders who trap Jodie Foster in a secured zone in the David Finch thriller "Panic Room" (2002). He also made the most of what might have been a clichéd role in "Phone Booth" (2002), playing an empathetic police captain who comes to the aid of a man (Colin Farrell) trapped in a telephone booth by a mysterious sniper.

Whitaker next moved into television, taking the reigns from Rod Serling as the host of UPN's revival of "The Twilight Zone" (2002-2003), executive produced the acclaimed TVT original film "Door to Door" (2002) starring William H. Macy, then appeared in the fact-based telepic "Deacons for the Defense" (2003) as the founder of the segregation-opposed organization of the 1960s who took up arms to oppose racial discrimination and battle the Ku Klux Klan. Meanwhile, on the big screen, the actor also served as a producer of the Latina-centric comedy "Chasing Papi" (2003), then, after coming close to directing a live-action version of Bill Cosby's animated series "Fat Albert" but ultimately departing the project, he moved behind the camera to direct Katie Holmes in "First Daughter" (2004), a lightweight tale of a headstrong, rebellious Presidential offspring who goes off to college and finds love with the undercover Secret Service agent secretly assigned to protect her (Whitaker also provided narration for the fairy tale-like production). The actor then signed on as a regular cast member for the fifth season of FX's "The Shield," playing a cop from internal affairs out to investigate Vic Mackey (Michael Chiklis) and his corrupt Strike Team.