In the summer of 1981, Alexander "Ned" Weeks, an openly gay writer from New York City, travels to Fire Island to celebrate the birthday of his friend Craig Donner at a beach house. Other friends in attendance include Mickey Marcus and the charismatic Bruce Niles, who has recently begun dating Craig, who is young and appears to be in good health. While walking on the beach, however, Craig feels dizzy and collapses. Later, when blowing out the candles on his birthday cake, Craig begins to cough repeatedly.
While traveling back to New York City, Ned reads an article in The New York Times titled "Rare Cancer Diagnosed in 41 Homosexuals". Back in the city, he visits the offices of Dr. Emma Brookner, a physician who has seen many patients afflicted with symptoms of rare diseases that normally would be harmless unless their immune systems had been compromised. All of these cases seem to be appearing in gay men. In the waiting room, Ned meets Sanford, a patient whose face and hands are marked with skin lesions caused by Kaposi's sarcoma, a rare cancer. Brookner examines Ned, but finds that he does not have the symptoms of this disease. She asks Ned to help her raise awareness of this disease within the gay community.
Craig suddenly suffers violent convulsions and is rushed to the hospital with Ned, Mickey, and Bruce where he is later pronounced dead. Brookner recognizes Bruce, noting that he is the former boyfriend of another one of her patients who recently died. Ned organizes a gathering at his home where many local gay men are invited to hear Brookner share information about the disease. Though she lacks conclusive evidence, she states her belief that the illness is sexually transmissible and that they should all avoid having sex for the time being to prevent new transmissions. Most attendees question her belief. She notes that few medical journals appear interested in publishing anything on this disease which is mostly affecting homosexual men. Ned announces that he wants to start an organization to spread information about the disease and provide services to those who have been infected.
Brookner and Ned visit a local hospital where several of her sick patients are in critical condition with an illness that is now being referred to as gay-related immune deficiency (GRID). They stay in rooms that many hospital staff are afraid to enter for fear of contracting the disease. Ned, Bruce, Mickey, and several other friends including Tommy Boatwright establish a community organization called Gay Men's Health Crisis (GMHC). The organization sponsors fundraisers for research on the disease now called AIDS and establishes a telephone hotline, counseling, and other services. Over Ned's objections, they elect Bruce their president. Ned arranges for his older brother, lawyer Ben Weeks, to provide free legal advice to the GMHC. The two brothers are close, but there remains an underlying tension over Ben's lack of understanding of Ned's sexuality. Ned contacts gay New York Times reporter Felix Turner, hoping that he can use his media connections to publish more stories about the unfolding health crisis. Felix laments that it is difficult getting any mainstream newspapers to report much information on AIDS. After Felix recalls that he and Ned had a sexual tryst at Man's Country bathhouse, the two begin a romantic relationship.
The disease continues to spread and claim lives. Tommy begins a ritual of taking the contact information of his friends who have died from AIDS out of his Rolodex and adding them to a pile, which he describes as "cardboard tombstones." Bruce attempts to travel to Phoenix with his boyfriend Albert, who is dying, so that Albert can see his mother one more time. The airline refuses at first to fly the plane with sick Albert on board. When they do eventually get to Phoenix, Albert dies following a period of dementia. The hospital doctors refuse to examine him and issue a death certificate, and instead throw his body out with the garbage. Bruce bribes a funeral home to cremate his body without a death certificate as Albert's mother sobs in anguish.
Brookner attempts to obtain grant money to continue researching AIDS, but her efforts are rejected by government officials who do not see AIDS as a priority. Ned, meanwhile, is kicked out of GMHC for his combative and aggressive tactics to promote awareness of AIDS, which is causing tension within the group.
Felix comes down with symptoms and his body wastes away as the disease claims his life. Felix arranges for a will with the help of Ben, and leaves everything he has to Ned. The two state their love for one another at the hospital before Felix dies. Upon hearing of Felix's death, Tommy solemnly adds his Rolodex card to his growing pile. A few days later, Ned visits his alma mater, Yale University, where a Gay Week is being hosted by the students. He admires how young men and women are able to dance with one another openly, without fear of discrimination.
Information is displayed about the growing number of people developing AIDS, as Tommy's Rolodex pile continues to grow, eventually including Bruce.
