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“There are still unanswered questions that need to be answered,” said Chief State’s Attorney Kevin Kane, who was the former New London County state’s attorney. “There is a big difference between probable cause and proof beyond a reasonable doubt.”

Joseph Reilly, 42, and Gary McAvoy, 46, had been charged with murder in 2005 by Norwich police in the brutal May 14, 2004, beating death of Eugene Mallove, 56, a scientist and writer from New Hampshire. Mallove was found outside his childhood home at 119 Salem Turnpike. His clothing was bloodied and disheveled, indicating a violent struggle.

Thursday’s dismissal of charges brought a smile to Reilly and tears to McAvoy, who took turns standing before Judge Susan B. Handy in a New London courtroom.

“It’s been a hard three-and-a-half years,” Reilly said. “All along we’ve said we’re innocent.”

McAvoy asked for a moment with his mother.

Both men are in prison on unrelated charges, but now are eligible for parole.

McAvoy and Reilly admitted to a crack-fueled burglary spree around the time of Mallove’s death, but denied any role in his slaying.

Defense attorneys William Koch Jr. and Jeremiah Donovan consistently had said state evidence in the case was seriously lacking.

Investigators, while gathering incriminating statements from jailhouse informants, had failed to connect the two men to the crime through any forensic evidence.

Koch, who represents Reilly, gave Kane credit for his handling of the situation.

“I would imagine the state doesn’t nolle too many murder cases,” Koch said. “It takes a lot of guts and courage.”

He shared a high-five with special investigator Tracy Wernicki. Both had spent countless hours poring over evidence. The two only recently discovered a mix-up with DNA evidence at the state crime laboratory.

Handy agreed to dismiss the case while preserving all evidence associated with it. Norwich police have said the case remains under investigation. Police Capt. Timothy Menard said they will continue to pursue all leads “with a fresh set of eyes.”

Mallove’s son, Ethan, said his family met with prosecutors earlier in the week and knew the dismissal was coming.

“Obviously we’re not satisfied with this,” he said. “Someone needs to be brought to justice. To have some form of closure seemingly within sight, and then suddenly retracted, has left us profoundly disappointed.”

Eugene Mallove was a Norwich Free Academy graduate who became the chief science writer at the Massachusetts Institute of Technology. He later dedicated much of his work to cold fusion and promoted experimentation in the field of alternative energy sources.

He founded the nonprofit New Energy Foundation in New Hampshire and published the magazine Infinite Energy, publicizing the work of others seeking alternative energy sources. He was cleaning out his rental property at the time of his death.

Members of the New Energy Foundation were astonished by the developments in the case, general manager Christy L. Frazier said Thursday.