The jury in the trial of two men accused of plotting to derail a Via passenger train travelling between Toronto and New York is now in deliberations.

The members of the jury were given instructions by Justice Michael Code before entering the jury room Wednesday, to decide the fate of Raed Jaser and Chiheb Esseghaier. Jaser is facing four terror-related charges, while Esseghaier is facing five. Not guilty pleas have been entered for both men.

Now that the jury has been sequestered, CTV News can report on what the jurors did not hear during the trial.

Here is a look at what the jury didn't hear:

-Just before the jury was selected, security officers rushed into the court as Esseghaier threatened to jump over the prisoner's box.

- Esseghaier does not recognize the Criminal Code of Canada, and wanted to be tried by the laws of the Qur'an.

-At one point, the judge scolded Esseghaier, telling him that he was making a fool of himself and should stop.

Still Esseghaier refused to be seated, with the judge eventually ordering him out of the courtroom and threatening to keep him in another room where he would watch the trial via closed circuit TV.

-Each day before the jury entered the courtroom, Code would put on the record that "Mr. Esseghaier objects to the jurisdiction of the court, sees himself as a sincere visitor who gives advice to the court and not as a criminal."

-The jury was also never told that, during three weeks of testimony, members of the public and the media never got to see the crown's star witness, an undercover FBI agent who was allowed to use the pseudonym "Agent Tamer el-Noury" when he swore an oath.

Instead, the media and the public were moved to another courtroom and watched the witness on a video feed, with the agent always out of the camera's lens.

The judge said in his ruling that this was to protect the "small number of undercover officers who are trained and are suitable for these kinds of (ongoing) investigations."

-The main courtroom was reportedly scattered with plain clothes police, giving the jury the impression that nothing was amiss.

-Esseghaier, who refrained from heckling the court in front of the jury, would fall asleep during the trial. When the jury was out, he would complain that he was tired because the jail guards gave him a blanket and two sheets to use to sleep. He said the sheets offended his religious sensibilities.

-Jaser, who has several fraud convictions, was arrested by immigrations officials in 2004. The officials unsuccessfully tried to deport the Palestinian national, who eventually acquired landed resident status.

Jaser's lawyers argued that he was never a serious terrorist, but rather a man who was trying to scam money from the FBI agent. The jury never heard about the fraud convictions.

With files from CTV Toronto's Austin Delaney