His career as an activist began in San Francisco during the turbulent 1970s when he was befriended by pioneer gay rights leader Harvey Milk. He worked as a student intern in Milk’s office while studying political science at San Francisco State University. In 1978, Milk was assassinated along with San Francisco’s Mayor George Moscone. Jones went to work in the district office of State Assemblyman Art Agnos.
In 1983, when AIDS was still a new and poorly understood threat, Jones co-founded the San Francisco AIDS Foundation. Jones conceived the idea of the AIDS Memorial Quilt at a candlelight memorial for Harvey Milk in 1985 and in 1987 created the first quilt panel in honor of his friend Marvin Feldman. The AIDS Memorial Quilt has grown to become the world’s largest community arts project, memorializing the lives of over 85,000 Americans killed by AIDS.
While in San Francisco, Jones took part in a documentary about the HIV/AIDS epidemic, speaking during World AIDS Day in 2005. In the documentary he talks about the idea behind the AIDS Memorial Quilt, as well as the activism of San Francisco citizens in the 1970s and 80's to help people affected by AIDS and to figure out what disease was. The film also looks at the impact HIV/AIDS is having in communities of color, and the young. The title of the film is "Echoes of Yourself in The Mirror".
Recently, Jones has been working with UNITE HERE, the hotel, restaurant, and garment workers' union on homophobia issues. He is a driving force behind the Sleep With The Right People campaign, which aims to convince GLBT tourists to stay only in hotels that respect the rights of their workers. Another part of Jones's work with UNITE HERE is making the labor movement more open to GLBT members.