The Crown announced in court Monday that it is proceeding by direct indictment against Raed Jaser and Chiheb Esseghaier.
The move means that the case is bumped up from provincial court to Superior Court without the step of having a preliminary inquiry. Such hearings are to determine if there is enough evidence for a case to go to trial.
Federal Crown attorney Croft Michaelson did not give a reason in court for the direct indictment, but did say he expected the trial would be "lengthy."
One of the charges was dropped on the new indictment. Esseghaier is no longer facing a charge of instructing someone to carry out an activity for the benefit of a terrorist group.
Esseghaier, a Tunisian national doing doctoral research in Quebec on nanosensors, is still facing five charges, with the addition of a third count of participating in a terrorist group. Jaser, a permanent resident of Palestinian descent, also had a participation count added and is now facing four charges.
Court also heard Monday that Jaser's lawyer, John Norris, is applying to get his client out on bail. The bail hearing has been set for Oct. 21.
Both Jaser, 35, and Esseghaier, 31, will be in court that day so a judicial pretrial, the next stage in the court process, can be set. Esseghaier has not applied for bail, as he still does not have a lawyer.
Esseghaier, sitting in the prisoner's box wearing an orange prison jumpsuit, repeated his now familiar refrain that he wants a lawyer who will use the Qur'an as a reference, not the Criminal Code.
"The only book is perfect is the holy book," Esseghaier said. "I don't accept any other reference other than the holy Qur'an."
Esseghaier said the Criminal Code is not perfect because it is created by humans, so he refuses to be judged by it.
Court has heard during previous court appearances that Esseghaier has met with lawyers and deemed them to be unwilling to run his case under his religious terms.
Superior Court Justice Ian Nordheimer asked about Esseghaier's current efforts to find such a lawyer. The process appears to be stalled.
"I always keep the door open for any lawyer who is able to help me," Esseghaier said.
Esseghaier has said that if he can't find a lawyer he is willing to represent himself, Michaelson told the court.
Esseghaier refused to be led away by a female court officer at the end of his appearance, telling her, "You are not my wife."
He said he did not want any woman who is not his wife to touch him, so a male court officer handcuffed Esseghaier and led him out of the court, while the female officer took Jaser, who had been seated in the jury box. He was wearing pants and a blue collared shirt. Jaser's family, including his father, has attended each of his court appearances so far.
Jaser and Chiheb Esseghaier were arrested in April and accused of plotting to attack a Via train that runs between Toronto and New York City. Police stressed at the time of the arrests that there was no imminent threat to the public.
The new indictment also narrows most of the allegations of terrorist activity from the scope of several months to several weeks.
Prosecutors had originally alleged Esseghaier and Jaser plotted together between April 1 and Sept. 25, 2012 and Esseghaier also participated in a terrorist group between Sept. 25, 2012 and Feb. 14, 2013.
Now, the Crown alleges both men conspired to murder for the benefit of a terrorist group and to interfere with transportation facilities for the benefit of a terrorist group between Aug. 26 and Sept. 25, 2012.
Participation in a terrorist group is also alleged from both Sept. 7 to Sept. 10 of that year and Sept. 13 to Sept. 24.
Esseghaier still faces the additional charge of participating in a terrorist group from Sept. 25, 2012 to Feb. 14, 2013.
If convicted, they could be sentenced to life in prison.
A third man, Ahmed Abassi, is facing terrorism charges in the U.S. and prosecutors allege he "radicalized" Esseghaier. American authorities also said Abassi did not support the alleged Via Rail plot and was pushing for a different plan that would contaminate the air or water with bacteria and kill up to 100,000 people.
Jaser is also fighting in Federal Court a decision by the Parole Board of Canada to revoke a pardon he had for unrelated crimes.
Jaser was granted the pardon in 2009 for uttering threats and fraud convictions from when he was a young man and Federal Court documents show that the parole board decided to revoke Jaser's pardon months after he was charged in the alleged Via plot.