The search for Savanah Nicole Soto and Matthew Guerra has come to a sad end, but the investigation into what happened is just beginning.

The pregnant 18-year-old and her 22-year-old boyfriend were found dead in their car on Dec. 26, four days after Soto's family last saw her alive, San Antonio police confirmed in a statement Wednesday, per the San Antonio Express News. They had both been shot and the unborn child also died, according to police.

A family member told CBS News that Soto, who was a week past her due date, had missed her Dec. 23 appointment at the hospital to have her labor induced.

"What we're looking at right now is a very, very perplexing crime scene," San Antonio Police Chief William McManus told reporters Tuesday. "Detectives are looking at this right now as a possible murder, but we don't know for sure. Because of the complex crime scene, we can't say for sure what we have."

At the time authorities had not officially confirmed the identity of the deceased and were waiting for the medical examiner's findings, but McManus said they believed it to be the missing couple.

The chief said police believed Soto and McManus had been dead for three or four days. Their car was spotted in the parking lot of an apartment complex in northwest San Antonio and it had been parked there for several days, McManus said. Someone who "came across the vehicle" alerted Soto's family and they called police, he noted.

McManus also declined to go into detail when asked what made it a "complex" scene.

Soto's mother, Gloria Cordova, said she last saw her daughter alive on the afternoon of Dec. 22, the Leon Valley Police Department told CBS News. Officers said they went to Soto's apartment for a welfare check later that day and were unable to access the unit, but seeing no signs of forced entry or other trouble, they left.

Leon Valley PD issued a CLEAR Alert (like an Amber Alert for missing or abducted adults in Texas) for Soto on Christmas Day.

"Ms. Soto, who is pregnant and has passed her delivery date, has caused significant concern among her family members after missing an essential medical appointment," the alert read. It also noted she might be in a gray 2013 Kia Optima with temporary Texas tags.

Soto and Guerra were found in the aforementioned Kia, according to McManus.

When Gloria couldn't reach her daughter on Saturday afternoon, she went to her apartment. "I went by there and knocked and knocked and knocked and she wasn't answering," Gloria told CBS affiliate KENS while the search was still ongoing. After not being able to contact Guerrra either, she filed a missing person report with Leon Valley police.

"My daughter is missing she was scheduled to be induced at 6:30 pm and never showed up," Glorida wrote on Facebook Dec. 23. "If you see her please reach out to me and lmk where you seen her. I'm worried about her safety she is w her boyfriend who is no good. Prayer for my baby girl."

Guerra's family reported him missing to San Antonio police, who sent the case to Leon Valley authorities, according to KENS.

"She was a good girl, she didn't deserve to go this way, especially with her baby," Soto's grandmother Rachel Soto told KENS on Tuesday night after the bodies were found. "He was an innocent child, nobody deserved this."

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