After divorce, Whalley returned to acting through making television films, including the 2000 television film Jackie Bouvier Kennedy Onassis in which she played the title character. She collaborated with the pop-punk band Blink-182 to read a letter at the beginning of the song "Stockholm Syndrome". In 2005, she appeared as Queen Mary I in The Virgin Queen, a BBC serial about the life of Queen Elizabeth I which also starred Anne-Marie Duff and Tara FitzGerald. The same year she also filmed Played which also starred her ex-husband Val Kilmer but the two did not share any scenes. In 2006, she appeared in Life Line, a two-part drama on BBC1, starring opposite Ray Stevenson. In 2008, she appeared in the ITV mini series Flood with Robert Carlyle amongst others.