Police believe the violence in Creggan, which led the the death of Lyra McKee, was 'staged and pre-meditated', a court has heard.
Derry Magistrate's Court heard further allegations that 51-year-old Paul McIntyre and 38-year-old Christopher Joseph Gillen were 'ringleaders' of the 'politically motivated' violence.
McIntyre, of Ballymagowan Park, and Gillen, of Balbane Pass, are jointly charged with riotous assembly, possessing a petrol bomb in suspicious circumstances and throwing a petrol bomb.
They are also charged with the arson of a Ford Transit tipper truck.
Gillen is further charged with the hijacking of the Ford Transit truck.
All the offences relate to alleged incidents on April 18.
The court was told that the evidence in the case involves footage from MTV, who had been in the Saoradh offices earlier that day and in Creggan as the violence unfolded, and video footage from and other media of the outlets and members of the public.
An investigating officer said that on April 18 police were conducting a search operation in Creggan when they came under 'sustained attack'.
He said that 'stones, petrol bombs and other missiles' were thrown at police.
The officer said the four vehicles were hijacked during the riot and three of them were burned out, including a Ford Transit tipper truck.
He told the court shots were then fired, one of which led to the killing of 29-year-old journalist Lyra McKee.
It is alleged that McIntyre and Gillen appeared on footage filmed by MTV at the Saoradh offices earlier that day and they were wearing 'matching' clothing to that worn by masked men involved in the violence.
The court heard that this clothing was not recovered during searches conducted of the defendant's homes.
Opposing bail, the officer said police had concerns the defendant's will re-offend or interfere with the 'massive' and ongoing investigation.
He said that there were a great number of young people in the area on the night in question and when members of the community attempted to intervene they were 'violently confronted'.
The officer also told the court that historically it has been difficult for witnesses in the Creggan area to come forward 'for fear of reprisal'.
He added that police have further concerns McIntyre and Gillen may flee the jurisdiction.
Derwin Harvey, defence solicitor for McIntyre, said there was a huge discrepancy between description given of the masked man and his clients appearance.
He said the evidence against the 51-year-old is 'extremely weak' and his client could spend up to a year on remand until the investigation is concluded.
Paddy MacDermott, defending Gillen, added the evidence is 'very tenuous' and nothing in particular stands out about the clothing the 38-year-old had been wearing earlier that day.
He said no one had come forward to police and named his client as one of the people involved in the riot.
The solicitor added Gillen's criminal record comprises of 'fairly minor offences' and that while police may believe he is a member of the New IRA there is 'no evidence to back that up'.
District Judge Barney McElholm said 'we are all aware of the disgraceful graffiti that appeared in Creggan threatening anyone who co-operated with police. Whoever did that did these two gentlemen a great disservice'.
The judge said he agreed with Fr Joe Gormley that 'all ideology is evil' and said that 'all nationalism, no matter what, evolves into fascism'.
He told the court that while there is no evidence the defendant's are members of a proscribed organisation, 'they are associated with an organisation, Saoradh, who have a very clear and defined ideology and they are not going to change that overnight'.
The judge said neither defendant has an appropriate bail address and no address within the city would be suitable.
He added that none of the objections could be managed by bail conditions.
The judge refused bail and McIntyre and Gillen were remanded in custody until May 30.