It was during the most recent police interview that Stephens told an officer he had sex with the woman but it been consensual.
Mr Patterson said at the time the woman was aged 19. She was now in her 40s and had children of her own.
The Crown say she was standing outside the nightclub known then as Pips on Vine St, about 2.35am on January 4, 1991, when she became separated from her friends.
She was then approached from behind by a man, who the Crown says was Stephens. He swore at her and put his arm around her shoulders, then across her throat so he was in control and marched her through the streets to the entrance to the Rose Gardens off Water St.
There they walked in the poorly-lit park, across a bridge, towards Second Ave where Stephens is alleged to have pushed the woman down some stairs onto a concrete pad.
"He threatened to kill her and because of that threat she complied. He raped her and he left," Mr Patterson said.
The woman grabbed her clothing, ran along Second Ave to a place then known as the Windsor Hotel where the owner raised the alarm and rang police. Police investigated and at the time it was reported as a "stranger rape" as the woman said she did not know the man and she never saw his face.
The woman was examined by a doctor and swabs for DNA taken. The samples were kept by the ESR. In 2004 Stephens gave a DNA sample to police as part of an investigation involving him driving with an excess breath alcohol level - that was also forwarded to ESR. In 2006 ESR and police put in place a system where DNA samples were compared with unsolved crimes, but it was not until 2010 that Stephens' DNA profile was matched to the DNA sample taken in 1991. It took a further three years before police tracked Stephens to a house in Taumarunui where they put the allegations to him.
Mr Patterson said Stephens then told Detective Wayne Pirret sex had taken place but it was with the woman's consent. "This case rests on the credibility of the complainant," Mr Patterson said.
ESR scientist Susan Vintiner gave evidence about the results of DNA samples and said the sample taken in 1991 was 3 million times more likely to come from Stephens than any other person in the New Zealand population.
Superintendent Sam Hoyle, who was a frontline constable in Whangarei in 1991, said the Rose gardens were not well lit and the place was frequented by people living rough.
"Because it was dark it often attracted those sorts of people" he said.
Arthur Fairley is representing Stephens and Judge John McDonald presides over the trial that is expected to last the week.