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The missing persons case was now a murder investigation. >> still a whodunit. we have no idea. >> reporter: the news media quickly picked up on the story. >> my husband told me. he saw it on the news. >> reporter: how did -- how did he tell you? what was the -- >> he came to my work and told me. and i just broke down. i couldn't believe it. >> reporter: police called the victim's best friend, debra. >> when they told me that they had found her body, i just collapsed to the ground. >> reporter: your friend melissa was dumped into a drainage canal. >> this beautiful, wonderful person who was not...

>> reporter: tony's attorney is bruce fleisher. >> they sought the death penalty. >> reporter: police and prosecutors were confident they had a solid case against tony villegas, but something happened that threw the whole investigation into freefall. that's because new crimes were about to be revealed. and new questions were about to be raised about who really killed melissa. and in the midst of it all, scott rothstein, like melissa, would disappear. >> coming up -- were melissa and scott rothstein's disappearances connected? >> we three kings be stealing the gold. >> the dark secret buried be...

Speculation about that woman in the firm who'd been killed. >> whether melissa knew about the ponzi scheme is one of those great mysteries. >> reporter: scott had started his ponzi scheme three years before melissa was murdered. >> is it time to take a fresh look at the whole melissa lewis murder? is there something more sinister? >> reporter: detective brian kendall now had a whole new problem with his fairly straightforward case against tony, the jealous train engineer. is this woman, melissa, killed because she knew too much? >> after we think we had this solid, buttoned-up case, "we do hav...

>> is it your wish to testify or remain silent? >> silent, sir. >> reporter: in closing arguments, prosecutor tate said all the evidence pointed to tony. the pepper spray, cell phone records, and the dna. >> there is not one other person on the planet earth that could leave the dna on this jacket. >> reporter: the defense reminded jurors that the pepper spray evidence was weak, and that both phone records and dna results could be manipulated. >> the pieces of the puzzle do not fall into place, because reasonable doubt prevents them from falling into place. >> reporter: the jury now had the cas...

He voluntarily answered them. he had been released from prison -- in the past. >> reporter: so you haven't ruled him out yet? >> not yet. >> reporter: with the list of possible suspects shrinking, detectives shifted their focus to something that might provide their first break in the case. with melissa's iphone missing, detectives put in an emergency request to the phone company to see if it could help track her cell. when he got the report, detective kendall couldn't believe what he saw. melissa's iphone had been active after the murder and someone had actually gone into her voicemail and pla...