After the case of Dr. Afia was issued  and became part of public discourse, the government of the United States claimed that she was arrested on 17 July 2008, which does nothing to explain her whereabouts since March 2003.

It is reported that she was brought to Pakistan in February 2008 to convince her to become a government witness against Khalid Shiek Mohammad - a high profile Al-Quaida leader and allegedly one of the masterminds of the September 11 attacks, who has been detained in Guantanamo Bay prison. As the case against Khalid Shiekh Mohammad is about to start the American forces need the assistance of Dr. Afia Siddiqui to convict him. Dr. Afia was allegedly severely tortured in Karachi, Pakistan in order to secure her compliance.

She was produced before a New York court where she had to be assisted into the hearing. It is reported that her health is in a serious condition due to the bullet wound she suffered after reportedly trying to attack one of her guards, but no medical assistance has been provided to her while she has been in American custody in New York.

According to the information received from a local human rights organisation in Pakistan, her kidney was removed while she was in custody in the United States. A closer look at the picture shows evidence of the years of physical abuse; there are dark circles under her eyes, and her nose was apparently broken at some stage and has been badly set. It is a picture of a severely dehydrated person in desperate need of medical attention.

In addition, although one son is with Dr. Afia but the whereabouts of her two other children still remain unknown. All three of her children were kidnapped along with Dr. Afia when she was taken by Pakistani intelligence officers on March 30, 2003. Her two children who remain missing were not with her when she was shifted to a governor's house in Afghanistan, for a brief stop over prior to her journey to New York, under heavy security. When she was being taken aboard a special plane there was no female security officer to provide support or assistance to her, and it was reported she fell down at least two times.