When investigators found the body of 49-year-old Kathryn Keener, she was unrecognizable.

She had been in a pond for days following her fatal shooting in 2009, and nature had washed away parts of her features and any forensic evidence investigators could have used.

That was one of a series of obstacles prosecutors said they experienced when investigating Keener’s murder, which led them this week to negotiate a plead deal with a suspect connected to the case.

Ronald McKinley, 29, of Greenland Road in Charleston, pleaded guilty Thursday to accessory after the fact of murder in Charleston County Circuit Court for getting rid of evidence following Keener’s shooting death.

Circuit Judge Markley Dennis accepted a negotiated sentence that puts McKinley on probation for five years. After working with the U.S. Attorney’s Office, state prosecutors made sure McKinley also will serve two years in prison for violating the terms of his release for a 2007 federal weapons conviction. That’s expected to happen in federal court next week.

The deal is infuriating for Paula Keener, Kathryn’s sister, who told The Post and Courier that she would have preferred to see McKinley go to trial.

“I can understand when a family is grieving it is difficult to feel satisfied sometimes with the results of the courtroom,” said 9th Circuit Assistant Solicitor Jennifer Shealy.

Shealy said the negotiated plea was the best course of action. But for Paula Keener, it was another blow for her in the case.

A December 2011 guilty plea from the man who pulled the trigger, 24-year-old Jessie James Murphy Jr., resulted in a 13-year sentence. That’s not nearly enough time for Paula Keener, who said the system failed to deliver adequate justice.

“The system didn’t fail me. The system failed a citizen of this state. Something has to change in the system for those who are going to find themselves in this situation after us,” Paula Keener said following Thursday’s plea.

It’s not over for her, she said, although she didn’t know how she intends to move forward yet.

Shealy is appreciative of the grief the Keeners have experienced and their devotion to the case, but she said everything prosecutors could do was done.

“We do not have the benefit of having an eyewitness or any confession that set out exactly what happened with Keener when she got shot, when she was put into the water and when the car was burned,” Shealy said. “That’s the trouble with the case.”

Investigators found Keener’s burned sport utility vehicle on Aug. 1, 2009, in the parking lot of a church on Wappoo Road.

A few days later, investigators found Keener’s body in a pond on Bear Swamp Road near West Ashley with one gunshot to the temple.

Keener’s relatives last heard from her before her mother’s birthday party on the day her car was found, an event she was supposed to be part of, but never showed up for.

Keener had a crack cocaine habit and had bought drugs from dealers in the Red Top area, according to prosecutors. On the day she was killed, she reportedly loaned her Toyota 4Runner to Murphy, which was a common practice for her to do in exchange for drugs.

To this day, Shealy said, they don’t have a confirmed motive for the killing. Another co-defendant in the case, Jamal Dover, 25 of Ravenel, has not gone to trial yet.