Over the next few days, more grisly discoveries are made - including another rib and vertebrae, a total of 20 bones. Then, finally, on June 9, investigators confirm that the remains are those of their daughter, Molly.
"I do know that Molly's in heaven and she doesn't have to suffer anymore," says Magi Bish.
The search for Molly Bish is over, but for her family, the search for Molly's killer feels more urgent than ever.
"This recovery of Molly hasn't ended anything. It's changed the focus of the investigation. We have to find this person, or he's gonna hurt someone again," says John Bish.
Investigators begin redoubling their efforts. But while the official investigators are still up on that hillside hunting for evidence, McGuigan is conducting his unofficial investigation five miles down the road - at the scene where Molly was abducted.
With him is criminal profiler John Kelly, who has developed a profile of the killer: "We felt he had to be a hometown guy because of the way Comins Pond is situated. He knew which roads to take. I mean this deed was carried out in an almost perfect way until her body was found."
Kelly also believes the man was no novice: "He wouldn't be as good. He wouldn't be methodical. 'Cause bear in mind this has been the perfect crime for three years. He got away with murder."
The discovery of Molly's body has already confirmed one of Kelly's predictions – that the killer would look for higher ground: "The reason for that is because if you go up on higher ground, doing whatever you're going to do to your victim, you can see people coming up, you can hear people coming up. So that gives you time either to escape or take off, or it gives you time to hide."
McGuigan and Kelly also visit Holly's crime scenes, and they are struck more than ever by the similarities in the cases, and the killer's profiles.
"This is obviously someone who knew the area extremely well, extremely well," says Kelly, who now believes 50-50 that these cases are connected. "I mean, this is really out of the way. I mean he obviously realized that he wasn't going to be interrupted."
Robert Armes, the man who McGuigan has kept coming back to for three years, becomes the focus of his investigation again.
Armes is a day laborer from Sturbridge who's since moved to a neighboring state. "I think that he's involved with Holly Piirainen," says McGuigan. "I'm not sure of any involvement with Molly Bish. I'm absolutely sure about Holly."
McGuigan says Armes knew the area well, and acted suspiciously after Holly's murder. He bought new boots the same day she was abducted, and then junked the car he'd been driving. "He knew about physical evidence. He wanted to get rid of physical evidence," says McGuigan.
But perhaps most striking of all is what Armes did shortly after Holly disappeared. He approached the family, volunteering to search and raise money.
In another strange move, Armes went to the press, declared himself a suspect, and denied any involvement: "I have a clear conscience. I don't need to confess to something I didn't do to have a clear conscience."
Police have never been able to determine Armes' whereabouts when the abduction took place, but they claim that he failed a lie detector test.
In the intervening years, McGuigan has taken statements from various people who know Armes, and claims to have overheard him implicate himself in the Piirainen murder.
As for the official investigation, State Police Lt. Peter Higgins says he's grateful for McGuigan's leads: "He has provided us information in the past, we've looked at it, we've worked on it, and it's proved helpful."
But so far, there just isn't sufficient credible evidence to justify an arrest. "Robert Armes knows what he did that day. He knows what he did," says McGuigan. "I'd like to talk to him."
After repeated requests for an interview, 48 Hours Investigates tracked down Armes in New Hampshire. Since moving there, Armes has been arrested numerous times on petty offenses, and pleaded guilty to assault against his own daughter.
Spencer asked Armes if she could ask him some questions about the Holly Piiranen case. He refused to answer. But McGuigan is still convinced that until Armes answers some questions, he can't be ruled out as Holly Piiraenin's killer.
There's far less evidence, however, to link him to the murder of Molly Bish. Armes vaguely resembles the first composite sketch of the mysterious "white car man," and witnesses put him in the area the week of Molly's disappearance. But other than the fact that he matches elements of Kelly's profile, there's little else to suggest Armes had any involvement.
"Can we say Robert Armes is responsible? Absolutely not," says Kelly. "We need to eliminate him, and he's certainly a person of interest who needs to be eliminated."
But wherever these investigations lead, McGuigan has certainly had an effect in refocusing the police's attention on them. "Even if I'm wrong, Molly Bish is still going home," says McGuigan. "There's a lot of activity being placed on these cases right now."
Nearly four years after Molly Bish disappeared, there's a permanent task force of several detectives still investigating her murder.
Police also say they're sharing information with the neighboring county, where Holly Piiraenin was killed, and still have not ruled out the possibility of a connection.
Meanwhile Tim McGuigan, the ex-cop who turned up key evidence in Molly's case, is trying to re-start his career officially. He's applying to become a police officer again.
And John and Magi Bish have been speaking to police all across the country, hoping to improve the way they handle missing child cases.