The coroner said the jury cannot find anyone at fault or apportion blame in their inquest verdict.
The jury was also shown CCTV footage which showed Noah naked as he cycled on a footpath outside houses close to where he disappeared.
His mother, Fiona, who sat alone in a corner at the back of the courtroom during the summing-up, left the hearing while the brief recording of the CCTV footage was played in the courtroom.
Rooney also reminded the jury that while most of Noah’s possessions and clothing were found, some items are still missing.
“We do not know what happened to Noah’s shorts and boxers,” he said.
His coat has also been missing since the day of his disappearance.
Rooney also stressed that the jury should arrive at their verdict by considering how things were at the time of Noah’s disappearance and death, and not with the benefit of hindsight.
The coroner also instructed the jury that their answers to the questions they are asked to consider must be unanimous.
The Judge’s charge to the jury comes after 62 days of evidence across a five-month period.
Since the end of January, the jury has heard evidence from 76 witnesses who took the stand in court or via video link while a further 42 witness statements were read out in court.
Noah Donohoe went missing after cycling across the city from his home off the Lower Ormeau Road in South Belfast.
He was last seen at Northwood Road in north Belfast close to waste ground where a culvert entrance to an underground water system is located.
He had abandoned his bicycle and was naked at the time.
The 14-year-old’s body was found six days later more than 600 metres downstream in the tunnel system.
The inquest has now adjourned and the coroner’s summing-up to the jury will resume on Monday 29 June before the jury goes out to consider its verdict.
