Although he had considered abandoning acting in favor of teaching, Emerson instead took the advice of a playwright-actor friend and enrolled in the MFA program at the Alabama Shakespeare Festival, where he spent three years honing his craft in “The Tempest,” “Much Ado About Nothing” and “Henry V.” Armed with his graduate degree, he opted to tackle New York once more, but most of the offers he received were for parts in regional theater. Finally in 1997, Emerson was hired for a supporting role in the off-Broadway play "Gross Indecency: The Trials of Oscar Wilde." When the performer tapped to play Oscar Wilde was fired, Emerson was tapped to play the lead. With glowing reviews, the production transferred to an off-Broadway theater and Emerson became touted as one to watch. Although he reportedly turned down a role in Michael Bay’s disaster flick "Armageddon" (1998) to remain with "Gross Indecency,” Emerson did accept supporting roles in "The Journey" (1997, which co-starred future second wife, actress Carrie Preston) as well as "The Impostors" and "Playing by Heart" (both 1998).

In the years after he first came to prominence in New York, Emerson continued to act on stage, including a turn opposite Uma Thurman in the off-Broadway staging of "The Misanthrope" (1998) and a well-received performance as Willie Oban in the revival of "The Iceman Cometh" (1999) starring Kevin Spacey. He went on to co-star with Kate Burton in "Give Me Your Answer Do" in a 1999 staging, then played George Tesman to Burton’s "Hedda Gabler" at Williamstown, then in Boston and Washington, DC, before finally settling on Broadway in 2001. In between those performances, Emerson essayed a memorable role as a confessed serial killer in several episodes of "The Practice.” As the seemingly mentally unbalanced William Hinks who may or may not have committed the murders he claimed, Emerson was nothing short of dazzling, earning him his first Emmy award for Outstanding Guest Actor in a Drama Series.

Emerson continued to churn out guest spots on series television, but had yet to find a home with a recurring or regular role. After episodes of “The Education of Max Bickford” (CBS, 2001-02) and “Law & Order: Special Victims Unit” (NBC, 1999- ), Emerson made the occasional foray into features with a small part in the Richard Gere-Diane Lane thriller “Unfaithful” (2002). Emerson popped up in guest starring roles on the long-running FBI procedural “Without a Trace” (CBS, 2002- ), the short-lived “Skin” (Fox, 2003-2004), Jerry Bruckheimer’s porn-centered take on “Romeo and Juliet,” and the ubiquitous “Law & Order: Criminal Intent” (NBC, 2001- ). Back in features, he had a small role in “Straight-Jacket” (2004), a period drama about a closeted 1950s actor (Matt Letscher) trying to keep the lid on his homosexuality by entering into a sham marriage to a naïve studio secretary (Carrie Preston). Emerson made a noticeable impact with his role as a sexually ambiguous orderly in the brutal horror flick “Saw” (2004).

In “The Legend of Zorro” (2005), Emerson had the tricky role of playing a fundamentalist Christian assassin who has a cross burned into his cheek and two pistols named Salvation and Damnation. Returning to television, he landed a guest spot on another short-lived series, “The Inside” (Fox, 2004-05), an FBI drama about a female profiler tracking down the most grisly of serial killers. It was in early 2006 during the second season of “Lost” that Emerson finally landed the role of a lifetime. Originally slated for three episodes as a captured member of the mysterious Others, Henry Gale, Emerson impressed the producers enough for them to write him into the show as a regular character. The seemingly innocent Henry Gale turned into the manipulative Ben Linus, the leader of The Others, by the end of season two. Straddling the line between good and evil, Emerson kept viewers guessing what Ben was up to and why he was manipulating the island’s castaways, adding a much-needed element of intrigue in a show that was seen by some as losing steam. His eerie portrayal earned the one time walk-on an Emmy award nomination for Outstanding Supporting Actor in a Drama Series.