NYT was the first to come up with an expose on Weinstein, detailing his almost three-decade-old history of sexual misconduct, which was followed by a more detailed report in The New Yorker.
Now a new article in The New Yorker has detailed how Boies personally signed the document directing Black Cube, a firm run by former ex-Mossad agents (the Israeli secret service), to uncover information that would stop the publication of any harassment stories about Weinstein in the papers including the New York Times.
In a statement posted on NYT's website, the paper said it was ending its association with Boies' firm.
"We never contemplated that the law firm would contract with an intelligence firm to conduct a secret spying operation aimed at our reporting and our reporters. Such an operation is reprehensible," the paper said.
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Boies also tried to address the controversy and said Weinstein was no longer a client of "mine or of the Firm".
"I did not (nor did the firm) select the investigators or direct their work; that was done by Mr Weinstein and his other counsel.
Boies said his decision to help Weinstein was a "mistake" and that he takes "responsibility" for that.
The article by Ronan Farrow detailed the length Weinstein allegedly went through to cover up his alleged misconduct.
He is said to have hired private investigators, including ex-Mossad operatives, to dig background information on women and journalists in an attempt to stop allegations against him from becoming public.