WATERVILLE — Authorities found a body on Wednesday in the apartment building of a missing woman who had last been seen putting her 8-year-old twin girls on a school bus Tuesday.

Melissa Sousa Photo courtesy of Maine State Police

Investigators from Waterville and Maine State Police discovered the body around 4 p.m. in the basement of the duplex at 32 Gold St., where Melissa Sousa lived with her boyfriend and their twin daughters. But police did not identify the remains as Sousa, the Maine State Police said in a statement late Wednesday.

Friends reported Sousa, 29, missing about 6 p.m. Tuesday, said Department of Public Safety spokesman Steve McCausland. Her boyfriend, Nicholas Lovejoy, 28, did not report her disappearance.

A friend said Lovejoy had previously threatened Sousa’s life, and Sousa was planning to leave Lovejoy and take their children with her.

“This is not like her to disappear,” McCausland said. “This is completely out of the ordinary.”

Detectives and evidence technicians spent several hours processing the crime scene before they removed the body shortly before 11 p.m. The remains were taken to the state Medical Examiner’s Office in Augusta for identification and an autopsy to determine cause and manner of death.

Lovejoy had been arrested around midnight Tuesday after Waterville police stopped an SUV he was driving on Summer Street, McCausland said in a news release.

Lovejoy was charged with having a loaded rifle in the vehicle and endangering the welfare of a child, because he had left his children at home alone, McCausland said.

“Lovejoy was interviewed at the Waterville Police Department this morning and has cooperated with investigators,” McCausland said. He was later taken to the Kennebec County jail, where he was being held in lieu of $2,000 bail.

Waterville police asked Maine State Police on Tuesday night for help in investigating the case, he said. Maine State Police investigate all homicides outside of Portland and Bangor.

Earlier in the day, police gave a physical description of Sousa and asked anyone who saw her or had information about her whereabouts to call police. Officers also searched a second location in Winslow.

But by the afternoon, police had swarmed 32 Gold St. as neighbors milled around on sidewalks, watching.

Nicholas Lovejoy Photo courtesy of Kennebec County jail

Debbie McDonald, 53, lives across Summer Street from where Lovejoy and Sousa live and said she told police she had heard five gunshots two nights ago.

“It freaked me out, it was so loud,” she said. “It literally sounded like it was in my yard. I looked out the window and didn’t see anything.”

McDonald said the developments on her street are “crazy.”

“It’s scary,” she said. “I was born and raised here and it used to be so good.”

Megan Legasse, Sousa’s friend and boss at Dunkin’ Donuts on Main Street in Waterville, said she and Sousa rode to work together every day and Sousa told her that Lovejoy, in front of their two children, had threatened to kill Sousa on several occasions.

“He’s locked her out of the house and pointed a gun at her while the girls were upstairs, looking out of the window,” Legasse said in a phone interview Wednesday. “A week ago in the driveway, he pointed a gun at her and the kids were saying, ‘Don’t kill my Mom.’ ”

Legasse said she last saw Sousa on Monday when Sousa dropped Legasse off at her home in Oakland. The two had talked about Sousa’s desire to leave Lovejoy and get her own place with her children.

An investigator with the Maine Warden Service stands in the middle of Taylor Road in Winslow on Wednesday as law enforcement officers searched for missing Waterville woman Melissa Sousa.

“She has Tuesday and Wednesday off and said, ‘OK, see you Thursday morning at 3 a.m.,’ Legasse recalled. “We had stopped at the bank so I could drop my deposit off and she went into the bank to get a loan to get an apartment.”

Legasse said Sousa was a good person and mother who was being threatened by her boyfriend.

She’s just stuck in a (bad) spot. She was threatened all the time. He threatened her. He said he had two options – to kill her, and to kill her.”

Legasse said a police detective came to her home Wednesday morning to talk to her, and she has been to the police department. She said Sousa has worked at Dunkin’ Donuts more than four years.

Legasse said Lovejoy and Sousa have been together about 15 years but are not married, and had come to Waterville from Massachusetts. Sousa has a brother in New Hampshire and her mother lives in Massachusetts, Legasse said.

“Her mom’s been telling her for days and days to leave. Nick knows where her mother is. He knows where everyone is.”