In 2009 the FBI believed that Coppola was going to turn state's evidence against the Genovese family and cooperate with the FBI. The FBI was willing to give him immunity from prosecution and enter him in the Witness Protection Program if he cooperated. The FBI believed he was involved in the killing of Lawrence Ricci (along with his son and stepson) on orders of Tino Fiumara, one of the men the FBI was hoping to prosecute with Coppola's cooperation. Coppola waived a speedy arraignment and spent the next two nights sleeping at FBI headquarters in lower Manhattan at an undisclosed hotel. He also met with a government arranged lawyer known as a shadow counsel. On the third day, however, Coppola refused to cooperate. His defense lawyer Henry Mazurek said that Coppola only dragged out the process out of concern for his wife, who he feared would also be arrested and charged.
In July 2009, Coppola was put on trial for murder, racketeering and extorting the Local 1235 of the International Longshoremen's Association for over 30 years. If found guilty of all counts, he could have faced life imprisonment. Defense lawyer Henry Mazurek told jurors that Coppola admitted to making a "rash" decision to flee, but that it didn't prove he's a killer. "He didn't want to stand trial for a murder he didn't commit," Mazurek said. Assistant U.S. Attorney Jack Dennehy told the jury not to be fooled by Coppola's claims and that Coppola "ran because he didn't want to face a jury like you. He hid because he didn't want to face a jury like you." Thomas Riccardi testified that Coppola said he did not agree with the Lardiere murder, but that he followed the orders given to him by Tino Fiumara (who was never charged). Genovese family member turned government witness George Barone was also called to aid the prosecution. Barone was such a difficult witness that the prosecutor apparently decided not to ask him about the Lardiere murder.
A witness to the murder, Raymond Zychlinski, was called on as a defense witness in the case. Zychlinski refuted the prosecutor's story that Lardiere's killer taunted him and said all he heard was a "horrifying scream". On July 21, 2009 Coppola was acquitted of the murder, partially due to the DNA test proving inconclusive since it matched 11 million white men in America. However, he was found guilty of violating the RICO Act for extortion and possessing false identification while he was a fugitive, which could have imprisoned him for up to 20 years. Coppola nodded and mouthed the words, "It's O.K.," to his wife after the verdict.
Coppola was then taken into custody already serving time for his original fugitive sentence in the Metropolitan Detention Center, Brooklyn. On December 18, 2009 Judge John Gleeson sentenced Coppola to 16 years in prison. He is currently serving his time at the United States Penitentiary, Atlanta and his projected release date is March 4, 2024.