Justice Ijeoma Ojukwu ruled that the duo be further detained by the DSS pending the hearing of their bail application on Friday.
Sowore was arraigned on a seven-count charge boarding on treasonable felony, cyber-stalking and transfer of illicit funds.
He pleaded not guilty to the seven counts when read to him.
Defence lawyer, Adeyinka Olumide-Fusika, urged the court to allow Sowore to be allowed to continue with the bail earlier granted him by Justice Taiwo Taiwo, on September 24.
The defence lawyer also pleaded that the second defendant be granted fresh bail.
But the judge said the bail earlier granted Sowore was not predicated on the charges on which he was arraigned on Monday, a fresh bail had to be granted to him.
Justice Ojukwu added that if she would have to grant them fresh bail, it had to be based on the formal written formal bail application and not oral.
She directed them to file formal bail application and subsequently adjourned hearing till Friday.
Sowore was arrested by the DSS Saturday, August 3 for planning a nationwide protest tagged #RevolutionNow.
The Nigerian government filed additional charges against Sowore on Friday, September 20, a day before the completion of the initial 45 days the court allowed the DSS to keep him in custody.
“What is interesting is that Boko Haram commanders who are engaged in high level terrorism have access to telephone, TV and even cable in their cells. So you wonder which one is better: a freedom fighter or a terrorist.”
He also said he has a bad shoulder following the way he was rough handled when arrested.