With jury selection set to begin in his murder trial, a South Elgin man accused of beating his girlfriend’s 3-year-old son to death pleaded guilty Tuesday to a lesser charge in a deal with prosecutors and was sentenced to 15 years in prison.

Jeffrey Johnson, 39, pleaded guilty to aggravated battery of a child in the May 1999 death of Matthew “Matty” Hodges. In return, prosecutors dropped a charge of first-degree murder.

Kane County State’s Attorney David Akemann said the plea agreement and sentence was the best prosecutors could do under the circumstances of the case.

Johnson could have faced life in prison without parole if convicted of murder.

Akemann said the case relied heavily on testimony from Matty’s mother, Cindy Hodges, who has been charged with seven counts of felony child endangerment for leaving Matty alone with Johnson.

She had agreed to testify against Johnson in return for having the charges reduced to misdemeanors and spending no time in jail.

“It was my judgement it was the right thing to do given the strength of the witnesses we would have had,” Akemann said. “This allows closure for the families and everybody to the extent that these kind of things can ever be closed.

Asked if he was comfortable with the plea agreement, Akemann said, “My head is, my heart isn’t.”

That explanation did not make the agreement any easier to swallow for Matty’s relatives, who cried as they watched Johnson smile at his parents, then walk back to a holding cell after appearing before Kane County Judge Donald Hudson.

“I think it stinks,” said Sue Pontanini, Matty’s paternal grandmother. “That baby can’t smile at his parents. He can’t eat. He can’t see the sunrise . . .I hope they beat him everyday (in prison).”

Prosecutors planned to argue that on May 16, 1999, Johnson hit Matty in the stomach, causing internal bleeding that led to the child’s death two days later, Assistant State’s Attorney Alice Tracy said.

Cindy Hodges has testified that Matty told her the day before he died that Johnson “apologized for hitting him accidentally in the stomach” a day earlier.

Johnson called 911 around 11:30 a.m. May 18 to report that Matty was not breathing. He later told police Matty drowned while taking a bath.

But paramedics said a cast on Matty’s leg and the sweat pants he was wearing were dry when they arrived at the apartment at 1000 Manchester Court, where Matty and Cindy Hodges lived with Johnson, Tracy said.

He also said the defense planned to provide medical evidence that the fatal injuries had to have been inflicted the weekend before Matty’s death – when Johnson was never alone with the boy.

“They jumped on the nearest, most available guy, and, unfortunately, that started this ball rolling.”

Even on Tuesday morning he briefly refused to leave his holding cell to appear in court.

“When you enter into a plea, you at least know what’s out there.”

Cindy Hodges, dressed in black and clutching Matty’s blanket and a stuffed Scooby Doo doll, rocked back and forth in her seat and cried as prosecutors described the evidence against Johnson.

Though she told the judge she agreed with the plea, she did not comment after Johnson’s court appearance. Earlier in the day Hodges said only that the last year has been difficult and that she “didn’t know what to think.”

In addition to aggravated battery of a child, Johnson pleaded guilty to unlawful possession of cannabis. Police said they discovered more than 30 grams of marijuana when they searched Johnson’s apartment the day of Matty’s death.

Prosecutors also agreed to drop a charge of unlawful possession of cannabis with intent to deliver.

A one-year sentence on the drug charge will run concurrently with the 15-year sentence. He will get credit for 474 days already served in Kane County jail. He will be eligible for parole in 13 years.

Akemann declined to comment Tuesday on whether the remaining charges against Cindy Hodges will be dropped.