Samson had been dropped off at the motel by a taxi driver at 1.43am on the night of the murder.
A person came to pick him up at 3.07am, leaving the motel at 3.24am.
"The Crown's case is between getting dropped off at the motel and about 3am that morning, the defendant murdered Azalia Wilson."
Thomas said Wilson was beaten to death.
"There were extensive blunt-force injuries to the head and face.
"It wasn't one punch, the Crown says it was from repeated blows, the force of such there was brain bleed, there were fractures of eye socket, nasal bones and jaw."
There were cuts all over Wilson's body.
The person who picked Samson up then drove him to the Oreti River, near Fosbender Park, to get rid of the evidence, the Crown alleges.
Thomas said evidence presented during the trial would show the key to the motel room was found at the river, as well as a handbag, purse and documentation belonging to Wilson. There would also be part of a knife, which linked back to a knife found in the motel.
"The Crown says that knife was taken out to the river because it linked the knife with her death."
A later search of the driver's car revealed a pair of boots that also had Wilson's DNA on them and matched impressions on her body.
Forensic evidence, CCTV footage and Ram data and phone evidence would be presented which would show Samson was at the motel, then travelled to the Oreti River before travelling to Christchurch where he only stayed for a few hours, Thomas said.
He then turned himself in to Invercargill police two days after the murder.
Defence counsel Judith Ablett-Kerr QC asked jurors to concentrate on the evidence.
"Focus on the evidence that you've got in front of you.
"Your duty is to come into the court with an open mind, to be independent and to listen to the evidence."
Of particular interest were the three witnesses who would be called tomorrow.
"These are central to the prosecution's case," Ablett-Kerr said.
Sixty-three witnesses will be called during the trial, which was expected to take between three and four weeks.
The trial continues tomorrow.
DO YOU NEED HELP?
If you're in danger now:
• Phone the police on 111 or ask neighbours of friends to ring for you.
• Run outside and head for where there are other people.
• Scream for help so that your neighbours can hear you.
• Take the children with you.
• Don't stop to get anything else.
• If you are being abused, remember it's not your fault. Violence is never okay
Where to go for help or more information:
• Shine, free national helpline 9am- 11pm every day - 0508 744 633 www.2shine.org.nz
• Women's Refuge: Free national crisis line operates 24/7 - 0800 refuge or 0800 733 843 www.womensrefuge.org.nz
• Shakti: Providing specialist cultural services for African, Asian and middle eastern women and their children. Crisis line 24/7 0800 742 584
• It's Not Ok: Information line 0800 456 450 www.areyouok.org.nz