LAS CRUCES, N.M. -

The latest details on an alleged child abuse case involving a Holloman Air Force Base couple accused of abusing and killing their 2-month-old daughter revealed the baby died with multiple injuries.

Police arrested Sgt. Peter John Zayas, 27, and Sophia Monique Zayas, 30, at the base last week.

According to court documents obtained by ABC-7, the baby died on Oct. 22, 2007. An autopsy revealed the baby had injuries to her head caused by shaking or blunt-force trauma, two skull fractures, 10 rib fractures and four lesions that investigators said were from cigarette burns. Medical examiners determined the baby died from multiple blunt-force trauma and ruled her death a homicide.

Investigators from the FBI and the Air Force said the Children, Youth, and Families Department took the couple's 2-year-old daughter, Anaya, away after they found she was developmentally delayed because of neglect. The court eventually took away the Zayas' parental rights to Anaya in 2010. Anaya is now in the custody of her aunt.

Investigators said the couple's stories on how their other daughter died have changed drastically over the years.

According to the document, when the baby died, the couple told investigators they had put her to bed after feeding her. The couple said when Sophia Zayas went to check on her about 30 minutes later, the baby's face was blue. She said she screamed for help and after attempting CPR, they called 911.

Investigators said the couple's reports of who put the baby to bed differed.

Now, after being arrested almost five years later, investigators said Peter confessed to killing his daughter, but his story did not match up with the medical evidence. When investigators told Peter that, he tried to change his story again.

According to court documents, investigators think Peter Zayas is trying to protect his wife who he said had a drinking "illness" and should not be held accountable for her actions.

Prosecutors said during the investigation, they learned Sophia Zayas is an alcoholic who acts out violently when she is drunk. They said Sophia Zayas lied to them by saying she hadn't had a drink in years and then later admitting she drank this year.

Investigators also said Sophia Zayas admitted to drinking the week the baby died and said that's why she didn't remember much of what happened. They said when they told Sophia Zayas how the baby died, she said she thought it was something like that.

After seeing each other for the first time since being arrested, court documents reveal Peter Zayas quietly told Sophia Zayas, "I did it." She responded, "That's a lie."

Elizabeth Martinez, the spokeswoman for the U.S. Attorney's Office, would not comment on why the investigation took so long to bring forth arrests. A prosecutor not involved in this case said it doesn't usually take nearly that long.

"We try and force it and make sure we get all those results and make sure the scientific evidence comes to us in order to charge it normally within weeks or a month or two, at the most," District Attorney Amy Orlando told ABC-7.

The couple pleaded not guilty in federal court on Wednesday. They are being held at the Doña Ana County Detention Center without bond until a continued detention hearing that will be held next week.

Peter and Sophia Zayas are both charged with one count of child abuse resulting in the death of a child and three counts each of child abuse and child abuse resulting in great bodily harm. If convicted of killing the 2-month-old, the couple could face life in prison.