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Cheryl Carter, accused of helping her ex-boss conceal material from police, said she had been asked by archivists to remove seven boxes marked as notebooks belonging to Brooks months earlier, but decided to get them when Brooks was on holiday on July 8, 2011.
This was the day after it was announced that Murdoch's News of the World tabloid was to be shut down amid anger at allegations its staff had been involved in phone-hacking and shortly after the paper's former editor Andy Coulson was arrested.
Carter and Brooks, the former boss of Rupert Murdoch's British newspaper arm News International, are charged with perverting the course of justice.
Brooks is also accused of conspiracy to hack phones and authorising illegal payments to public officials, charges she denies. Coulson and four others are also on trial over similar accusations which they deny.
The Old Bailey jury heard that Carter had asked the company's archivist, Nick Mays, to get the boxes from storage on July 8.
The boxes, placed in the archive in 2009, were marked as containing Brooks's notebooks from 1995 to 2007, during which time she had been editor of both the News of the World and Murdoch's daily Sun tabloid.
In a recorded interview with police, played to the jury, Carter said she had been asked by Mays to remove material from the archive as it was downsizing.
She said she had decided to deal with the boxes that week in July because Brooks was on a "boot camp" holiday, where she would be at home with a personal trainer.
Carter, who worked as Brooks's assistant for 16 years, arranged for her son Nick and Brooks's driver to help take the boxes from the archives. Her son then took them back to her house.
She said the seven boxes mainly contained her belongings. There were just three notebooks, a diary and photographs belonging to Brooks, which she said she returned to the company's offices.
"I threw away the rest of the stuff," she said.
In the interview, detectives read out a statement from Mays in which he said he had not asked Carter to remove any material from the archive, adding it indicated a "sinister" explanation for her actions.
"I understand what you are saying but it is not like that," she replied.
Earlier her lawyer told the court police had also suggested that she was offered a job on a Murdoch paper in Australia as a reward for helping Brooks hide the notebooks.
However, her son told the jury that the family had been planning to emigrate and had had visas from 2007. They had gone ahead with the move in early 2012, but had to abandon the project after Carter was arrested.
Carter, who said she went to school with Brooks's first husband Ross Kemp, said Brooks had let her write a Sun beauty column and sobbed as she told police Brooks had got her son a job as an editorial assistant at News International after he had gone through a bad stage with acne.
Brooks was very kind and fair, but also tough, Carter said. "She shouted quite a lot of time," she added.