Sheriff's investigators found Silliman's body on the bathroom floor of an empty mobile home near New Hill in southwestern Wake County on December 3, 2008.
According to the medical examiner, the Eagle Scout was drugged, strangled and suffocated.
Detectives have accused four former friends in his death: Aadil Shaaid Kahn, 18, Allegra Rose Dahlquist, 19, Drew Logan Shaw, 18, and Ryan Patrick Hare, 19.
Dahlquist and Khan were classmates at Apex High School with Silliman at the time of his death while Shaw was a sophomore at Panther Creek High School. School officials have said Hare withdrew from Panther Creek earlier in 2008.
All of the defendants, except Hare, were under 18 at the time of the alleged murder.
In court Friday, Hare entered a not guilty plea to the charges against him. In a plea deal with prosecutors, Dahlquist entered a guilty plea to the lesser charge of second-degree murder and will testify against Hare.
"She's accepting responsibility for what she did," Dahlquist's attorney Joe Cheshire said.
Prosecutors say Dahlquist was romantically involved with Hare. Authorities say they believe Hare was upset after learning about a relationship between Dahlquist and Silliman.
"Mr. Hare became jealous of this new relationship," Assistant District Attorney Jason Waller said.
Prosecutors say Hare developed a plan to kill Silliman and got Dahlquist, Shaw and Kahn to help out.
The plan allegedly started with a car ride on November 25. Prosecutors say Hare tried to strangle Silliman with a zip tie that day while riding around Wake County.
"That attempt did not work," Waller said. "There was a taser in the car, the taser did not work it was supposed to immobilize Mr. Silliman."
At one point, they say Silliman got out of the car.
"But because he was with his friends and trusted his friends, he got back into the 4-Runner," Waller said.
They eventually ended up inside a vacant home owned by the Dahlquist family that they used for storage. Five days later, while Dahlquist distracted Silliman with tarot cards, Hare allegedly hit him in the head with a hammer.
"That hammer did not phase Mr. Silliman," Waller said.
Partly because, prosecutors believe, Silliman had been drinking wine laced with horse tranquilizers and eventually, he became very groggy.
"At that time his hands were zip tied in front of him and his feet were zip tied," Waller said.
Authorities say duct tape was placed over Silliman's mouth, a plastic bag over his head and a zip tie around his neck.
"We believe the evidence will show that Ms. Dahlquist put that zip tie around his neck with the bag over his head and Mr. Hare came later and tightened that zip tie," Waller said.
They say that resulted in Silliman's death.
"It's all immensely senseless," Cheshire said.
As part of the plea deal, Dahlquist has agreed to continue cooperating with investigators.
The judge also agreed to combine all the charges against Hare into one trial that's expected to begin in mid-September.
Kahn and Shaw were not in court Friday, but in the past, lawyers have said they are also expected to agree to plea deals in exchange for testifying against Hare.
Court documents obtained by ABC11 last year indicate one of the suspects confessed to Apex Police, leading two others to admit to the killing.
Silliman was first reported missing by his parents on Nov. 26 and authorities had issued a Silver Alert for him. He was last seen less than 10 miles from the mobile home where his body was found.