At MIT, Mitchell served as an advisor to MIT President Charles Marstiller Vest in guiding a decade-long, five-building expansion project at the university that included designs by Charles Correa, Frank Gehry, Steven Holl, Fumihiko Maki and Kevin Roche, and added one million square feet of classroom, office and other spaces to the MIT campus. The building project became the subject of his 2007 book Imagining MIT: Designing a Campus for the 21st Century, which was written in a single weekend while he was at a Dublin hotel. At the dedication ceremonies for the Frank Gehry-designed Stata Center in 2004, Mitchell said that schools like MIT "carry a particular responsibility to conceive of architectural projects not just as the rational allocation of resources to achieve quantifiable management goals, but also as inventive, critical contributions to our evolving culture" and that anything less would be "a betrayal of their advertised principles".
Starting in 2003, he created the Smart Cities program within the MIT Media Lab. Projects that Mitchell developed as part of the Smart Cities program included GreenWheel, a device that would add electric power to a bicycle; RoboScooter, a foldable electric scooter; and the MIT Car (also called the "CityCar"), which would be propelled by electric motors built in to its wheels. The car and scooter projects were envisioned as being made available for public use at locations in cities, with access and scheduling controlled by computer. The MIT Car was designed to fold up into a more compact shape while parked.