After being punched and attacked with a metal pole, the 30-year-old was tied up and thrown into a car boot before being driven to a property outside Lakes Entrance in eastern Victoria.
Mr Lyons remained trapped in the boot for hours while a group of people plotted their next steps from inside a nearby disused water tank.
They wanted him to confess to allegations he sexually assaulted children, prosecutors told the Victorian jury on Thursday.
Mr Lyons was eventually taken out of the boot and tied to a massage table, where he was tortured, before being locked inside the boot again.
The next time he felt fresh air, Mr Lyons was thrown into a shallow grave and shot dead.
Three months later, in March 2019, police were led to dense bushland, where they found his remains.
Jordan Bottom, Rikki Smith and Albert Thorn are facing a Supreme Court trial, charged over Mr Lyons' December 2018 death.
All three are charged with murder, assault and unlawful imprisonment.
Bottom has pleaded not guilty to all charges.
Thorn has pleaded guilty to false and unlawful imprisonment, and intentionally causing injury, but denies assault and murder.
Smith has admitted intentionally causing serious injury, but denies unlawful imprisonment, assault and murder.
Prosecutor Raymond Gibson alleged the attack was planned by Thorn and another man in the days before.
Before arriving at Mr Lyons' house, Thorn visited a camping store and purchased two balaclavas and two rolls of duct tape to restrain the man, Mr Gibson said.
He said Thorn arrived at the property just before 1pm, where he was later joined by Smith and two others.
The four men went to the back door of the house and walked to the master bedroom, where Mr Lyons was recovering from a night of shift work.
"They then immediately set upon the unsuspecting Lyons who was lying on the bed," Mr Gibson told the jury
"The men proceeded to seriously assault Lyons."
After this Mr Lyons was thrown into the car boot and taken to a rural property where he was tortured.
Mr Gibson alleged Thorn, Bottom and Smith put him back into the boot and drove him to Double Bridges, where they placed him inside a shallow grave and shot him in the leg and head, killing him.
"The three men buried Lyons and left the area," he said.
The prosecution and defence openings will continue on Friday, in the trial before Justice Andrew Tinney.
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