In the end, they didn't know if they were a woman or a man:
"In 2004, Arquette expressed an interest in undergoing gender-transitioning medical treatment. She decided against undergoing hormone therapy and kept her choice of whether she underwent gender-affirming surgery private from the media by the time she completed her transition in 2006. Her experience was documented in the film Alexis Arquette: She's My Brother, which debuted at the 2007 Tribeca Film Festival. Arquette was a vocal supporter of other transgender people, including Chaz Bono, who transitioned shortly after Arquette.
Arquette contracted HIV in 1987. In later life, Arquette suffered from ill health as a result of being HIV-positive. Amid these increasing complications, Alexis began presenting again as a man in 2013. Brother David Arquette said that Alexis was "gender suspicious" and alternately felt like a man or a woman at different times.
Arquette was placed in a medically-induced coma and died on September 11, 2016, surrounded by close family, at the age of 47. Arquette was serenaded with David Bowie's "Starman". The official cause of death was cardiac arrest caused by myocarditis stemming from HIV."