Baker left the private sector in May 2008 to volunteer on Obama's campaign, serving on the technology, media, and telecommunications policy group. After the president's election, Baker served on the technology, innovation, and government reform and the VA review teams for the transition team. Baker is active in the federal technology community, and has written extensively on improving the management and results of the government's IT investments. He was vice chair of the Industry Advisory Council's Transition Study Group, and a co-author of the group's capstone paper entitled "Returning Innovation to the Federal Government with Information Technology."

The VA's IT infrastructure has been in the spotlight since May 2006 when a laptop computer containing the social security numbers of 26.5 million U.S. veterans was stolen from an analyst's home. Several months later, a computer containing the personal information of up to 38,000 veterans went missing. The computers have since been recovered but the agency has been under a microscope by members of Congress. In the final years of the Bush administration, VA IT chief Robert Howard appeared on Capitol Hill routinely to discuss the agency's efforts to streamline and secure its technology.