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According to the newspaper, former Deputy Attorney General Rod Rosenstein had ordered former special counsel Robert Mueller to examine "any links and/or coordination between the Russian government" and Trump's campaign, but former law enforcement officials said that privately, Rosenstein told Mueller to conduct only a criminal investigation.
The revelation is likely to fuel new scrutiny from Democrats who have long argued that the scope of the President's ties to Russia have yet to be fully examined without interference.
Mueller had documented extensive evidence in his final report in March 2019 that Trump tried to obstruct the Russia investigation in multiple ways, and declined to make a charging decision. A Justice Department policy said that a sitting President could not be indicted.
Former FBI deputy director Andrew McCabe, who had opened the counterintelligence investigation, told The Times that Rosenstein had never told him about his decision.
"We opened this case in May 2017 because we had information that indicated a national security threat might exist, specifically a counterintelligence threat involving the President and Russia," McCabe said.
"I expected that issue and issues related to it would be fully examined by the special counsel team. If a decision was made not to investigate those issues, I am surprised and disappointed. I was not aware of that."
Just a criminal investigation, McCabe told the paper, was the wrong approach for the situation.
"It was first and foremost a counterintelligence case," he said. "Could the President actually be the point of coordination between the campaign and the Russian government? Could the President actually be maintaining some sort of inappropriate relationship with our most significant adversary in the world?"
The Times report comes one week after the Senate Intelligence Committee released the most comprehensive and meticulous examination to date explaining how Russia interfered in the 2016 presidential election and the Trump campaign welcomed the foreign adversary's help, revealing new information about contacts between Russian officials and associates of Trump during and after the campaign.
Unlike Mueller's report, which focused on questions of criminal conduct, the committee's report detailing the findings of its counterintelligence is hundreds of pages of facts the panel obtained, drawing conclusions in places where Mueller often stopped short of doing so.
