In 1987, Jones became executive director of the Names Project Foundation (NPF), which raised the money required to store, move, and display the quilt around the world. The NPF was nominated for the Nobel Peace Prize in 1989.

In 1994, Jones was himself diagnosed as HIV-positive. He resigned as director of the NPF, and was given the position of founder and spokesperson and guaranteed health benefits for the remainder of his life. In 2001, the NPF relocated its offices and the quilt, which now weighs some 50 tons, to Atlanta.

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However, Jones and the new administration of NPF did not agree in regard to some basic policies, and in 2004, when he complained publicly, he was dismissed from his position.

Jones had always felt it important to display the quilt in different locations, so that a wide variety of people could see it. The new leadership of NPF, Jones asserted, only sought to create a museum to house the memorial.

Jones filed suit against NPF, alleging wrongful dismissal. His suit asked that NPF be placed in receivership and that the quilt be returned to San Francisco and once again be deployed in the fight against AIDS.

After being accused of reneging on their promise to provide Jones with life-time health benefits, NPF promised that it would honor its agreement.

In December 2005, the suit was settled, with each party receiving some satisfaction. Jones was awarded 280 of the original quilt panels for display around the San Francisco Bay Area under the management of a new organization, San Francisco Friends of the AIDS Memorial Quilt. He was also granted sole discretion to nominate four people to fill two new positions on the NPF board of directors. Further, NPF agreed to provide an official link to his organization on their web site.

For its part, NPF was granted the right to manage the remainder of the quilt as it sees fit.

In 2004, Jones became director of the Los Angeles SHANTI Foundation. SHANTI, named for the Sanskrit word for inner peace, offers practical and emotional support to people with life-threatening or chronic diseases. In his new position, Jones continues his community-based activism.

Among the awards Jones has received is the Harvard AIDS Institute's AIDS Leadership Award.

In the United States, glbtq people have played an integral and often leading role in AIDS activism, greatly influencing AIDS treatment and advocacy.

In response to the AIDS epidemic, a number of activist groups, including Gran Fury and the NAMES Project AIDS Memorial Quilt, have used art as a means to raise awareness about the epidemic.

Marches on Washington in support of the rights of glbtq people have been a significant part of the modern movement for equality.

San Francisco has enjoyed a reputation as a "gay mecca" since World War II.

Harvey Milk, the first openly gay man to be elected to public office in the United States, was assassinated in San Francisco's City Hall, making him the American gay liberation movement's most visible martyr.