Secret Story explores further cultural integration than Metheny’s previous Brazilian-centered albums with Pat Metheny Group during the 1980s. The opening song, «Above the Treetops», is an adaptation of a Cambodian spiritual song; other pieces take influence from East Europe, such as «Antonia». Japanese pianist and singer Akiko Yano appears on «As a Flower Blossoms», earning the only co-writing credit on the album. Yano had previously collaborated with Metheny thrice; on «Lots of Love» from her 1991 album LOVE LIFE; and two Metheny covers: «‘It’s for You'» on Welcome Back (1989) (which also featured Metheny performing on two additional songs) and «Praise» on Super Folk Song (1992). Orchestral arrangements for the album were conducted by Jeremy Lubbock.
Metheny took Secret Story on a concert tour, and a video recording of a live performance at New Brunswick, NJ, was issued. This film, also called Secret Story, was re-released on DVD in 2001.