A onetime Navy diver at Pearl Harbor pleaded not guilty Tuesday to charges that he struck his young son on multiple occasions over a year’s time and then fatally injured the boy on Sept. 18, 2009, by striking him on the head and shaking his body.

Engineman 2nd Class Matthew McVeigh is charged with two specifications of murder, two specifications of manslaughter, and assault in the death of 14-month-old Brayden McVeigh, the Navy said.

A general court-martial trial was expected to take place in early December, but ongoing evidence gathering and scheduling conflicts may push the date back, officials said.

McVeigh was a diver assigned to SEAL Delivery Vehicle Team 1 at the time of his son’s death, but has since been reclassified an engineman.

At the pretrial hearing Tuesday, a defense attorney unsuccessfully sought to sever the assault charge from the remaining charges at a future trial, meaning the assault charge wouldn’t be heard at the same time as the murder and manslaughter accusations.

Defense attorney Cmdr. David Norkin said he believed the probability of an assault conviction to be "exceedingly remote" because the charge is "ridiculously weak."

Norkin referenced 16 to 17 injuries to Brayden, including bruising and two separate broken arms, but he said there is no actual evidence to link any harm to Matthew McVeigh.

Brayden’s mother, April, who is not charged, had more than her share of "alone time" with the boy, Norkin said.

If the assault charge and the history of injuries were tried at the same time as the murder and manslaughter charges, jurors would believe Matthew McVeigh had a predisposition to injure the child, he said.

"They would be using the assault charge to prove the murder charge," Norkin said of the government prosecution.

Lt. James Toohey, part of the prosecution, said Matthew McVeigh found out from a doctor that Brayden had received a shoulder injury, but told a new babysitter the boy had a reaction to ear infection medicine — circumstantial evidence that Matthew McVeigh inflicted the injury.

The judge hearing the request, Capt. David Berger, denied the defense motion to sever the charges.

Norkin at one point said one doctor may testify in the case that Brayden died of natural causes, and that Matthew McVeigh doesn’t have an explanation for how his son died.

Matthew and April McVeigh, their daughter, Brodi, then 3, and Brayden were the only people home when Brayden was brought upstairs, not breathing and limp in his father’s arms, on Sept. 18, 2009, April McVeigh said at a preliminary hearing in May.

Brayden died later "as a result of intracranial injury due to abusive head trauma," the autopsy found. The severe brain injury could have been caused by shaking and/or impact, the report said.