"We had a priest with a sexual predilection for young boys," said prosecutor Martha Coakley, "a priest who told his victims, in this case the young boy that he was abusing, that if he told he would not be believed."
For weeks, jurors listened carefully to tense exchanges between the accuser and the former priest's lawyer.
At times, the accuser broke down on the stand as he testified in graphic detail how Shanley pulled him out of Sunday morning catechism classes and molested him in the bathroom, the rectory, the confessional and the pews. The abuse started when he was 6.
He is perhaps the most notorious figure in the sex scandal that rocked the Boston Archdiocese nearly three years ago.
The accuser, now 27, put his head down and sobbed as the verdicts were read after a trial that hinged on the reliability of what the man claimed were recovered memories of decades-old abuse.
The verdict was no surprise, says CBSNews.com Legal Analyst Andrew Cohen.
"The jury believed the victim, who testified in great detail and with heart-wrenching emotion, and was not swayed by the lone defense witness, an expert, who testified that recovered memories were not accurate," Cohen said.
Jurors believed memories can be repressed, said juror Victoria Blier, 53.
"We agreed after discussion that you can experience something up to a point, and then not think about it and have plenty of other things in your life that are more important," she said.
"Jurors are naturally very sympathetic to victims in these cases and very skeptical of medical or psychological testimony that tries to explain away the allegations," said Cohen.
Shanley, 74, showed no emotion as he stood next to his lawyer. Bail was revoked and he was immediately led to jail.
Blier said she and fellow jurors were swayed by the accuser, believing the man would not have come forward if he wasn't telling the truth.
"I think a persuasive sentiment was he had already gotten a half-million-dollar settlement and he had no reason whatsoever to pursue this criminal case, and he knew that pursuing the criminal case was going to lay a painful life bare," she said.
Shanley, once a long-haired, jeans-wearing "street priest" who worked with Boston's troubled youth, sat stoically for most of the trial, listening to his accuser's testimony with the help of a hearing aid.
The accuser had said that he repressed his memories of the abuse but that they came flooding back three years ago, triggered by media coverage of the scandal that began in Boston and soon engulfed the Catholic church.
"When you are young you often have no vocabulary for dealing with sexual abuse. You have no way therefore to process that abuse," said Coakley.
Shanley's conviction on all four charges gives prosecutors an important victory in their effort to bring clerics to justice for decades of child sex abuse at parishes across the country.
The defense called just one witness — a psychologist who said recovered memories can be false, even if the accuser ardently believes they are true. Shanley's lawyer also argued the accuser was either mistaken or concocted the story to cash in on a multimillion-dollar class-action settlement between the archdiocese and abuse victims.
The accuser, now a firefighter in suburban Boston, was one of at least two dozen men who claimed they had been molested by Shanley.
Three years ago the church's own records showed that archdiocese's leaders knew about allegations against Shanley, reports CBS News Correspondent Trish Regan. It's believed he molested some two dozen children. But rather than remove him from his post, Shanley was simply transferred from parish to parish.
Rodney Ford, whose son also had accused Shanley of abuse, called the verdict "a relief for my son, and all the other victims."
Shanley's niece disagreed, saying "There are no winners today. There are only losers. We're no closer to finding out the truth about this scandal or finding out what happened."
Frank Mondano, Shanley's lawyer, planned to appeal.
"It appears that the absence of a case is not an impediment to securing a conviction," he said.
Cohen doesn't think much of Shanley's prospects on appeal.
"The defense chose to put only one witness on the stand and the trial was not so complicated that any particular ruling by the judge swayed it one way or the other. So I don't see this verdict being overturned on appeal," he said.
Typically, priests facing sex abuse crimes from long ago are not prosecuted, because the statute of limitations has, most often, run out. Many abuse victims see this verdict as their own victory, reports Regan.
"It says that there can be some justice. So many of us had to count on this case for our own justice because our cases could not be brought to court, said Ann Hagan Webb of SNAP the Survivors Network of those Abused by Priests.