In a pre-trial hearing on Thursday, her lawyers, led by Charles Swift, argued that Dr Siddiqui could only be tried on terrorism charges in the US, and not on murder charges. In this regard, he quoted various international regulations.
But US District Judge Richard Berman ruled out the motion, saying that the US courts have jurisdiction if American citizens were subjected to attacks abroad, citing some precedents.
But Ms Siddiqui, who is languishing in a maximum security jail, interrupted her lawyers in US District Court in Manhattan to announce that she did not plan to participate in her trial, scheduled for Jan 19.
I am boycotting this trial, she declared. I am innocent of all the charges and I can prove it, but I will not do it in this court.
Since the very beginning, Ms Siddiqui has said that she has no confidence in the American judicial system or the lawyers appointed for her by the court - even those retained by the government of Pakistan - and that she wants to make peace and knows how to do it.
She has vigorously protested against what she called humiliating strip searches before she is brought to the court.
Judge Berman said that her trial would proceed after her lawyers and prosecutors visit Afghanistan to interview eyewitnesses to finalise their case.
Lawyers for Ms Siddiqui tried to convince the court that she was mentally incompetent to stand trial, citing in part her refusal to cooperate with lawyers and the reports of a psychologist who said she suffers from delusional disorder and depression.
Judge Berman rejected that argument after prosecutors pointed to psychological reports that concluded she was faking mental illness.
Berman on Thursday rejected defence arguments aimed at tossing out charges against Ms Siddiqui that carry a potential minimum prison sentence of 30 years and a maximum penalty of life in prison.
Before he ruled on the request, Dr Siddiqui said visits by her lawyers were torture for me and it was a waste of money for lawyers to go to Afghanistan to interview witnesses because she was not participating in the trial.
Im not dealing with them anymore, Dr Siddiqui said of her lawyers. Theyre just people coming to my door and talking, talking, talking.
During a break, Dr Siddiqui was led out of the courtroom by US marshals when she would not stop talking loudly. Take me out, she said. Im not coming back.
She was not present when the judge made his decision.