After the verdict was read, Judge Jeannine Barr sentenced Nelson to life in prison. Prosecutors had not sought the death penalty.
Nelson was accused of kidnapping Jonathan on Christmas Eve 2010. His burned body was later found wrapped in carpet, discarded in a ditch.
Nelson had told police she dumped the contents of a garbage can there, but claimed not to know that they included the boy's remains.
The entire trial lasted a little more than two weeks. It culminated in dramatic closing arguments on Monday. And by Tuesday morning, the judge reached her verdict.
A bench trial, rather than a jury trial, is an unusual choice in capital murder case, but both sides say that's what Nelson wanted. In the end, it wasn't the verdict Nelson hoped for, when she asked for a bench trial.
"When the judge found her guilty, she told the judge, 'I'm innocent your honor, I'm innocent,'" said defense attorney Allen Tanner.
Prosecutors Connie Spence and Sunni Mitchell spent two weeks methodically building their case, with multiple witnesses, cell phone records, and even grainy surveillance video. Taking no chances, even though they only had to convince a judge of one instead a jury of 12, that Nelson was guilty of murder.
Jonathan's mother was not in court Tuesday morning, but prosecutors spoke with her after the verdict was announced.
"I just talked to her on the phone and she let out a whoop of you," said Spence. "She felt very satisfied. Obviously, this is not in any way going to diminish her missing her child, but the fact that someone is held responsible, I think she's very, very grateful for."
Victims' advocate Andy Kahan says Jonathan's story resonated with many.
He said, "Frankly, Jonathan became Houston's child. He will always be remembered in that vein. It could be anybody, on any day, there but by the grace of God, go I."
The capital murder conviction means Nelson automatically gets a sentence of life in prison without parole, though her attorney says an appeal is already underway.
"We believe someone else kidnapped this child and someone else killed this child," Tanner said. "I do not believe Mona Nelson committed this offense."
Prosecutors obviously disagree, giving much of the credit for the conviction to the Houston Police Department for the amount of investigation officers put into this case.
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