A jury considering the case of three people accused of killing half of their family over honour absorbed mountains of evidence over about 10 weeks, but they weren't privy to all the details of the trial.

Deliberations have started in the Shafia family murder trial and what took place in court outside the presence of the jury can now be reported.

The Crown decided not to call evidence that patriarch Mohammad Shafia brought out a knife in a fight with a family member at the time of the funerals for the alleged victims in this case.

Shafia, 59, his wife Tooba Yahya, 42, and their son Hamed, 21, are charged with four counts each of first-degree murder. They're accused of killing three of Shafia and Yahya's daughters — Hamed's sisters — and Shafia's first wife in a polygamous marriage.

Zainab, 19, Sahar, 17, Geeti, 13, and Rona Amir Mohammad, 50, were found dead June 30, 2009, in a car submerged at the bottom of a canal in Kingston, Ont.

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Geeti, Zainab and Sahar Shafia were found dead with their father's first wife, Rona Amir Mohammad, in June 2009. (Trial evidence)

During the trial, some of the family's relatives testified for the Crown, alleging they heard threats from Shafia that he would kill Zainab, and some testified for the defence, saying the family is innocent. Both accused parents took the stand, and during Yahya's testimony, she started talking about a time when one of her brothers — who had earlier testified for the prosecution — "jumped on" Shafia and tried to hit him.

Crown attorney Gerard Laarhuis cut her off and suggested the jury leave the courtroom. After they were gone, he explained Yahya had been veering into evidence they had to agreed to exclude.

There was an incident at the time of the funerals that saw Shafia bringing out a knife in a scuffle with a brother of Yahya, Laarhuis told Judge Robert Maranger.

"We agree that that's really not relevant to these proceedings and its prejudicial (nature) outweighed its probitive value," Laarhuis said.

Order banning contact

The jury was also unaware that there had been an order banning Shafia, Yahya and Hamed, who sat in the prisoners' box side by side each day, from communicating with each other. Maranger vacated that order Jan. 17 after the jury was excused, once Shafia and Yahya's testimony was over and it was clear Hamed would not take the witness box.

But on Dec. 14, just before court took a break for the holidays, it seemed all but certain that Hamed would testify. His lawyer Patrick McCann told Maranger after the jury was sent home that he would be calling his client to the stand. It's not clear at what point between then and the end of Yahya's five days of brutal cross-examination that a different decision was made.

The jury was similarly unaware of an order preventing the accused family members from communicating with the surviving children. Until a surviving son testified on their behalf in court, he had not seen his parents and brother since July 21, 2009.

Maranger lifted that order on Dec. 14, after the son's testimony and after the Crown conceded the risk of influencing witnesses had passed.

At one point, Shafia's lawyer Peter Kemp indicated, without the jury present, that he would be calling both the son and another surviving sibling to testify. But at some point between when he said that on Dec. 9 and the next week, following a withering two-day cross-examination of the son, it became clear the sister would not take the stand.

She did appear in court, though, on the last day of her mother's cross-examination. On Jan. 16, the young woman rushed into the courtroom just as the jury was exiting for a break, cried out and pressed her lips to the glass of the prisoner's box. The jury saw this, and saw Shafia put his lips to hers through the glass, but they were not made aware of who she was.

After the jury left, a court security officer warned her not to approach the prisoners' box again, especially with the jury still in the room, and she sat down on a court bench and made loud weeping sounds, though when she stood up a few minutes later her eyes were dry. She was in court along with another surviving Shafia child on the last day of court.

The accused family members had also been prevented from speaking with Moosa Hadi, an engineering student-turned interpreter-turned private investigator, court heard before the jury was in one day.

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A view of a lock at the Kingston Mills Locks where a Nissan Sentra was found with the bodies of Zainab, Sahar and Geeti Shafia, and Rona Amir Mohammad, inside in June, 2009. (Lars Hagberg/Canadian Press)

Studying at Queen's University in Kingston, Hadi read about the case after the arrests and offered to be an interpreter between the lawyers and their clients, as he too was originally from Afghanistan. Shafia hired him on the side, court heard, to conduct a parallel investigation, and he developed a fervent belief in the family's innocence.

He received the same disclosure from police as the lawyers and made an audio recording of a jailhouse conversation with Hamed, in which Hadi claims Hamed reveals the truth of what happened four months after his arrest.

Hamed said he was at the canal and witnessed his four relatives plunging into the water in a car. He said he honked the horn of his car once then dangled a rope in the water, but seeing no signs of life, he drove away and told no one. The Crown suggested the story was a "complete fabrication."

During Hadi's testimony — he was called as a Crown witness — the judge excused the jury while the lawyers argued about asking Hadi about intercepted communications of the Shafias in their native language of Dari. Maranger ruled he would not allow the defence to pursue the area, saying Hadi was biased.

"He's clearly an agent of the accused," Maranger said. "He worked for the accused and continues to do so in his own mind. That makes him wholly unqualified to give unbiased testimony."

Sent emails to lawyers, reporters

During the trial Hadi sent emails addressed to the lead investigator in the case and copied to reporters and the lawyers.

In one, he stated that he wished to report a "criminal activity" committed by Laarhuis in his cross-examination of Yahya.

"He was trying to obstruct the justice by diverting the attention of the judge and public from his own criminal activities including unlawful imprisonment of innocent people for 2.5 years," Hadi wrote. "Under the so-called 'cross-examination' he was playing with dates and distances only to find a discrepancy in Mrs. Yahya's testimony by confusing her."

Hadi wrote that he expected when he first reported his findings to police in 2009 that Shafia and Yahya would be released, after investigators realized their "obvious errors."

Shafia and Yahya were dragged "to the verge of committing suicide" by being subjected to this prosecution and the fact that they are still breathing today, "there is no exaggeration if I claim it is because of my efforts," Hadi wrote.

"As a result of these criminal activities, ignorances, bias and stupidities dominated in this case I have suffered from PTSD."