A judge will soon decide if the sailor will be tried with the baby's mother or separate.
NewsChannel3's Darragh Copley was the only reporter in the courtroom as the two appeared in court.
The prosecution presented a timeline on how 6-month-old Brayden Whalen died while in the care of his mother's boyfriend, Andrew Lundsford.
His mother, Brittany Whalen, prosecutors believe knew about the abuse and did nothing to stop it.
December 28th, 2012, Lundsford moves into Brittany's apartment according to testimony.
The next day, evidence presented in court shows pictures of baby Brayden with a bruise over his left eye.
Then on January 1st, a child abuse expert testified that baby Brayden's injuries were consistent with traumatic abuse suffered the same day that he was brought into the hospital.
Lundsford told detectives he slapped the infant twice but gave several different versions as to how Brayden ended up in intensive care.
Detectives told the court that Lundsford sent cell phone pictures of the bruises to Whalen texting her that the baby had fallen beginning on December 29th.
The Hampton investigator said that Whalen told him that she was an experienced EMT worker and looking at the picture she knew her son had not just fallen.
Still in court, NewsChannel 3 learned the mother still let Lundsford care for the baby by himself days after seeing the first bruise including January 1st, the day doctors believe Brayden suffered the traumatic brain injury that ended up killing him.
One detective told the court that Whalen even said, "I knew this was going to happen."
The judge certified the child abuse and neglect charges for both while Lundsford faces the additional murder charge.
Now a circuit court judge will decide if the former couple should be tried together or separately next month.