The government's theory was that MacDonald had "got into a fight with his pregnant wife because his youngest daughter, Kristen, had wet the bed; that he picked up a club to strike his wife and accidentally struck and killed his daughter, Kimberley, who was trying to intervene; and that then, in order to cover up his accidental misdeed, killed his wife and then mutilated and killed his youngest daughter and tried to make it look like a cult slaying," court papers said.
Prosecutors argued that the wounds MacDonald suffered, including stab wounds and a punctured lung, were either self-inflicted or the result of his struggle with Colette.
MacDonald was found guilty and sentenced the three life sentences for the murders.
Statements made by Stoeckley's mother and by a former U.S. deputy marshal are two key pieces of evidence the defense said they would like to have examined in this appeal.
Stoeckley's mother, Helena, swore in a 1997 affidavit before she died that "on two separate occasions, my daughter confided in me that she was present in the MacDonald house on February 17, 1970."
She also said her daughter told her they decided to go to MacDonald's house originally to intimidate him because they felt he was being too hard on drug users in the Fayetteville, N.C., area.
MacDonald was known to counsel and see drug users in his position as medical officer at Fort Bragg, and in his private practice in the Fayetteville area, according to court documents.
Jimmy Britt, who was a U.S. marshal at the time of the trial, underwent a polygraph test in 2005 when he stated that he overheard the prosecutor during the trial, Jim Blackburn, pressure Stoeckley to change her testimony, including telling her she would be indicted for murder if she testified she was inside the MacDonald home at the time of the killings.
The polygraph administrator found no deception evident in Britt's statements, according to court papers.
Another retired deputy, Lee Tart, said in an 2005 affidavit that Britt told him in the fall of 2002 something that had been troubling him about the MacDonald case.
"He said Helena Stoeckley told him that she had been in the MacDonald house on the night of the murders. He said Helena Stoeckley told Jim Blackburn, the prosecutor, the same things during his interview with her," Tart said.
"Mr. Britt told me thereafter Jim Blackburn told Helena Stoeckley that if she testified to these things in the courtroom he would indict her for murder," Tart said.
Britt and Stoeckley are both dead, however, and prosecutors said in court papers that allowing those statements without live testimony would be "improper."
The government also argued that the DNA crime scene evidence MacDonald wants allowed should be excluded, because it is not among the items authorized for appeal.
MacDonald did not attend the hearing today, remaining in a federal prison in Maryland, but his wife told the AP he would like his medical license back if he is exonerated and freed.