In 1996 McCune appeared opposite Brett Climo who played her brother in Blue Heelers, in a friend's film The Inner Sanctuary. In early 1997 she played the role of Anne in the Melbourne Theatre Company's (MTC) production of Sondheim's A Little Night Music. In 1998, McCune played Cinderella in another Sondheim musical, Into the Woods. She also did two short seasons of the classic two-hander Love Letters. In early 1999 she took six weeks off Blue Heelers to play one of the leads, Mary Abacus, in the miniseries adaptation of Bryce Courtenay's The Potato Factory, which earned her a nomination for an AFI award for Best Actress in a TV Drama. In July 1999, a couple of months before finishing on Blue Heelers, she starred alongside John Wood in She Loves Me. Later career (2000–present) Immediately after finishing Blue Heelers, she starred alongside John Waters, Bert Newton, Nikki Webster, Rachel Marley and later Rob Guest in a stage version of The Sound of Music, as Maria von Trapp. In 2001, while she was pregnant with her first child, her portrait by Shaun Clark was entered in the Archibald Prize. She was off screens for a year to be a stay-at-home mother. In 2002, her next project was a "comeback" role in the television series Marshall Law with Alison Whyte and former Blue Heelers cast member William McInnes. Although it rated well in the first week, the series was critically panned and its subsequent low ratings ensured it was cancelled after one season. In 2004, after another year off due to the birth to her second child, McCune slowly began to return to television. She again was the advertising face of Coles Supermarkets. She also hosted Seven Network shows The World Around Us and Forensic Investigators. McCune also appeared as the love interest opposite Matt Day in the ABC telemovie Hell Has Harbour Views. In September 2005, McCune guest starred in a four-episode storyline on MDA alongside her former Blue Heelers co-star Paul Bishop. Also in 2005 she narrated a second season of Forensic Investigators and appeared in the Australian film Little Fish, starring alongside Cate Blanchett and Sam Neill in the early stages of her third pregnancy. In 2006, she played Annabel in Tripping Over. She has also appeared in a number of musicals and other stage productions around Australia, notably as Sally Bowles in Cabaret, Hope Cladwell in Urinetown,