Sophie's either sixteen years in the making or nearly three depending on whether you go back to the beginning or not. The beginning was at The Voyager Company, an early electronic publisher (The Criterion Collection, Robert Winter's CD-Companion Series, Who Built America, Pedro Meyer's I Photograph to Remember and Laurie Anderson's Puppet Motel etc.). Back in 1992 Voyager released the Expanded Books Toolkit (explained by Douglas Adams) which enabled people to make simple e-books without any programming. The first three titles were Martin Gardner's Annotated Alice, Douglas Adams' trilogy Hitchhiker's Guide to the Galaxy and Jurassic Park (before it came out in paperback). The second three were Marge Piercy's Gone to Soldiers, Susan Faludi's Backlash and perhaps the first text-based "double-feature" which paired Neil Postman's Amusing Ourselves to Death with Aldous Huxley's Brave New World.
Shortly thereafter, Voyager Japan released T-2 which has gone on to become the leading ebook software in its home country. In 1996 a group of Voyager employees formed Night Kitchen with the intent of creating an authoring/reading environment that would extend the Expanded Books Toolkit concept to include rich media. The result TK3 never officially came to market, but teachers in high schools and colleges used it in their classrooms and with their students created some remarkable projects.
The Mellon Foundation approached some of the TK3 team and asked them to build a new multimedia authoring program which would be open-source and would extend TK3 by enabling time-based events (e.g. a timed, narrated slide show or embedding links at specific points in video clips). That became Sophie.