Stein then worked with Alan Kay at the Atari Research Group on various electronic publishing projects.
After Voyager, Stein founded Night Kitchen to develop authoring tools for experimental electronic publishing, primarily TK3[permanent dead link].
Stein is the director of the Institute for the Future of the Book. According to Stein: "The Institute has two principal activities. One is building high-end tools for making complex electronic documents (part of the Mellon Foundation's higher-ed digital infrastructure initiative). The other is exploring and hopefully influencing the evolution of new forms of intellectual expression and discourse." This new scholarly direction is being explored under the umbrella of MediaCommons.
In 2019 Stein donated his archival papers and hard drives to Stanford University.[1]