By that time, bodies had been buried and some blood stains had been scraped from the walls, Special Agent Matthew Hoffman of the Army's Criminal Investigation Command said.
Other stains remained, on walls and floors. Investigators also recovered shell casings consistent with the weapons Staff Sgt. Robert Bales reportedly carried and a piece of fabric similar to the blanket prosecutors say he wore as a cape during the killing spree.
Hoffman testified during the third day of a preliminary hearing for Bales, who is accused of slipping away from his remote post at Camp Belambay in the middle of the night to commit the killings.
The hearing, which is expected to feature testimony from some Afghan soldiers and villagers Friday and Saturday nights, will help determine whether his case advances to a court martial on counts of premeditated murder.
Hoffman arrived at Belambay to investigate just hours after the March 11 massacre, but he and his colleagues were unable to reach the two villages where the killings occurred. An angry crowd of local residents gathered outside the post, he said, and any time they could see an American soldier, they became enraged.
Afghan investigators got out to the scenes that day, where they engaged in a firefight. They recovered some evidence and took photos that they turned over to U.S. authorities. But Hoffman and his colleagues didn't visit until April 2, and even then they feared ambush.
"We were fully expecting to be attacked at any time," he said.
He also said Bales tested positive for steroids three days after the killings.
Bales, a 39-year-old Ohio native and father of two from Lake Tapps, Wash., leaned back in his chair at the defense table and betrayed no reaction as an Army doctor, Maj. Travis Hawks, gave clinical descriptions of treating the wounded villagers as they arrived at a nearby forward operating base.
One young girl had a large bullet wound in the top of her head, he said. She was unresponsive at first, but survived after treatment.
A woman had wounds to her chest and genitals, but she and her relatives insisted that the male doctors not treat her. Prosecutors displayed photos of the victims being treated.
Earlier Wednesday, a friend testified that Bales seemed remorseful after being taken into custody. Defense witness 1st Sgt. Vernon Bigham testified by video from Kandahar Air Field in Afghanistan.
A prosecutor, Lt. Col. Jay Morse, has said Bales spent the evening before the massacre at his remote outpost of Camp Belambay with two other soldiers, watching a movie about revenge killings, sharing contraband whiskey from a plastic bottle and discussing an attack that cost one of their comrades his leg.
Within hours, a cape-wearing Bales slipped away from the post and embarked on a killing spree of his own, Morse said. He attacked one village then returned to Belambay, where he woke up a colleague and reported what he'd done, Morse said. The colleague testified that he didn't believe Bales and went back to sleep.
Bales headed out again, Morse said, and attacked the second village before returning once again in the pre-dawn darkness, bloody and incredulous that his comrades ordered him to surrender his weapons.
Bales has not entered a plea, and is not expected to testify. His attorneys, who did not give an opening statement, have not discussed the evidence, but say Bales has post-traumatic stress disorder and suffered a concussive head injury during a prior deployment to Iraq.
Bales has not participated in a medical evaluation known as a "sanity board," because his lawyers have objected to having him meet with Army doctors outside their presence.