Raed Jaser and Chiheb Esseghaier are each facing four terror-related charges while Esseghaier is also facing a fifth separate terror charge.
Justice Michael Code spent three and a half days delivering 300 pages of instructions to jurors who will decide the verdicts in the case, ending with a call for them to carefully consider all they have seen and heard in court.
"You have taken an oath to try the charge and render a true verdict according to the evidence," he said. "If you honour that oath you will have done all that's expected of you."
The trial, which began on Feb. 2, heard hours of secretly recorded conversations between Jaser, Esseghaier and an undercover FBI agent who gained their trust while posing as a wealthy American businessman with radical views.
The wiretaps formed what Code considered the most important evidence in the case.
The court heard conversations in which Jaser and Esseghaier discussed their alleged radical ideologies, the alleged plot to derail a train travelling between New York and Toronto and other ideas for potential terror plots which would be in retaliation for Canadian military actions in Muslim countries.
Crown prosecutors argued there was an "overwhelming" amount of evidence against the two accused, and urged the jury to find them guilty on all counts.
Jaser's lawyer, however, argued that the permanent resident of Palestinian descent was only feigning interest in the alleged terror plot as part of an elaborate con to extract money from his co-accused and the undercover officer.
Jaser did not take the stand in his own defence.
Esseghaier, a Tunisian national who was pursuing a PhD in Montreal when he was arrested in 2013, chose not to participate in his trial because he wanted to be judged by the rules of the Qur'an.
He did not cross-examine any witnesses or bring a defence, but he did offer the jury what he considered "sincere advice" in an usual written closing statement, urging them to follow the rules of the Qur'an and prepare for "judgement day."
Esseghaier, who has frequently fallen asleep through portions of the trial, also provided several comments on the proceedings to Code, in the jury's absence.
At one point on the day before jurors began deliberating, Esseghaier emphatically told Code that people had been killed by God in the past because they didn't follow his rules.
"You're still talking about killing plots and you forgot that God himself killed a lot of people in the past, because of their wrongdoing," he said. "When I invite you to apply the laws of God that are written in the holy Qur'an ... it is for your own good...because God is severe in his retribution."
While the jury didn't hear the colourful remarks Esseghaier made from the prisoner's box, Code nonetheless reminded jurors they had to consider the evidence in the case with an open mind.
He reminded them that "no adverse inference" could be drawn from Jaser's decision to remain silent and Esseghaier's decision not to participate in the trial.
"Remember you are judges, you are not advocates for one side or another," he said. "You must consider all the evidence when you determine whether Mr. Esseghaier and or Mr. Jaser committed an offence alleged in the indictment, always remembering that the onus is on the Crown to prove guilt beyond a reasonable doubt."
Code also reminded jurors to weigh the evidence presented in the case "as a whole."
"You must not examine evidence piecemeal," he said. "Your inferences should be rational or logical and not conjectural or speculative."
Jurors were also warned not to think of the consequences their verdicts might bring for the accused.
"You should not be influenced by any outside consideration including the subject of punishment," Code said. "Your objective is to decide your verdicts ... based on what you've seen or heard in this courtroom."