Stone was at Apple Computer from 1986 to 1993, working on multimedia hardware, software and publishing. In her last year at Apple, Stone worked for CEO John Sculley on special projects. In 1993, Stone joined Microsoft Research under Nathan Myhrvold and Rick Rashid. She co-founded and directed the Virtual Worlds Group/Social Computing Group, researching online social life and virtual communities. During this time, she also taught as adjunct faculty in New York University's Interactive Telecommunications Program. In 2000, she became a Microsoft vice president, working on industry relationships and improving Microsoft's corporate culture. She left Microsoft in 2002.