Details released from US courts in November showed the FBI relied on the existence of 36 illegally copied movies as evidence of willful law-breaking. The FBI told the US courts Megaupload had been told of the illegal files in 2010 and the continued existence was evidence to flagrant criminality.
However, Dotcom's lawyers said the files were kept at the request of the US government which asked it do nothing to impact on its criminal investigation. They claimed FBI testimony to secure arrest warrants managed to "exclude critical facts" which would have shown the company's efforts to assist. Instead, they gave a "selective distorted account" and "deliberately misled the court".
The filing says Megaupload was painted by the FBI as a "brazen scofflaw" and the files were the only linking thread which tied together those described by the FBI as the "Mega Conspiracy".
It also pointed to other court cases which showed warrants being declared invalid if the applicant - in this case the FBI - was shown to be dishonest or reckless.
The help sought in 2010 related to a Homeland Security investigation into NinjaVideo, a file-sharing site which used Megaupload's system to store files. An agent on the case contacted Megaupload's data storage company Carpathia to ask for help securing the files. Megaupload was told not to alter or change the files - a detail not later mentioned by the FBI.
Mr Dotcom's lawyers pointed to an email between Carpathia and Megaupload from 2010 as capturing the reality. The email, from Carpathia executive Phil Hedlund, detailed the search warrant issued to capture the NinjaVideo material.
Mr Hedlund said the warrant was restricted to just Caropathia and Megaupload but would be otherwise kept secret. He said it was possible to do so "because we relayed to the Government Mega's willingness to work with the Government for these types on requests". He added: "We have no reason to believe the Megaupload is the target of the investigation."
The Weekend Herald revealed the details around the so-called double-cross in November when the first US court files were unsealed. Mr Dotcom, waiting on the US to comply with NZ court orders for discovery, said: "I understand why the US is working so hard to appeal the discovery decision."
He said Megaupload worked hard to comply with requests to remove unlawful material.
"We have always co-operated. We have responded to takedown requests, we have been a good corporate citizen."