WASHINGTON — The Justice Department secretly took steps in 2017 to narrow the investigation into Russian election interference and any links to the Trump campaign, according to former law enforcement officials, keeping investigators from completing an examination of President Trump’s decades-long personal and business ties to Russia.
The special counsel who finished the investigation, Robert S. Mueller III, secured three dozen indictments and convictions of some top Trump advisers, and he produced a report that outlined Russia’s wide-ranging operations to help get Mr. Trump elected and the president’s efforts to impede the inquiry.
But law enforcement officials never fully investigated Mr. Trump’s own relationship with Russia, even though some career F.B.I. counterintelligence investigators thought his ties posed such a national security threat that they took the extraordinary step of opening an inquiry into them. Within days, the former deputy attorney general Rod J. Rosenstein curtailed the investigation without telling the bureau, all but ensuring it would go nowhere.
A bipartisan report by the Republican-led Senate Intelligence Committee released this month came the closest to an examination of the president’s links to Russia. Senators depicted extensive ties between Trump associates and Russia, identified a close associate of a former Trump campaign chairman as a Russian intelligence officer and outlined how allegations about Mr. Trump’s encounters with women during trips to Moscow could be used to compromise him. But the senators acknowledged they lacked access to the full picture, particularly any insight into Mr. Trump’s finances.
Now, as Mr. Trump seeks re-election, major questions about his approach to Russia remain unanswered. He has repeatedly shown an openness to Russia, an adversary that attacked American democracy in 2016, and refused to criticize or challenge the Kremlin’s increasing aggressions toward the West. The president has also rejected the intelligence community’s finding that Russia interfered in 2016 to bolster his candidacy and the spy agencies’ assessment that Russia is trying to sabotage this year’s election again on his behalf.
Mr. Rosenstein concluded the F.B.I. lacked sufficient reason to conduct an investigation into the president’s links to a foreign adversary. Mr. Rosenstein determined that the investigators were acting too hastily in response to the firing days earlier of James B. Comey as F.B.I. director, and he suspected that the acting bureau director who approved the opening of the inquiry, Andrew G. McCabe, had conflicts of interest.
Mr. Rosenstein never told Mr. McCabe about his decision, leaving the F.B.I. with the impression that the special counsel would take on the investigation into the president as part of his broader duties. Mr. McCabe said in an interview that had he known Mr. Mueller would not continue the inquiry, he would have had the F.B.I. perform it.
“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,” Mr. 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.”
Mr. Rosenstein declined to comment. The disclosure about the counterintelligence investigation is based on interviews with former Justice Department and F.B.I. officials.
Installing Mr. Mueller as special counsel in May 2017, Mr. Rosenstein ordered him to examine “any links and/or coordination between the Russian government” and the Trump campaign. Many Democrats embraced the appointment as a sign that law enforcement would complete a full accounting of Mr. Trump’s ties to Russia.
But privately, Mr. Rosenstein instructed Mr. Mueller to conduct only a criminal investigation into whether anyone broke the law in connection with Russia’s 2016 election interference, former law enforcement officials said.
“I love Ken Starr,” Mr. Rosenstein told Mr. Mueller, according to a new book by the journalist Jeffrey Toobin that first reported the conversation. “But his investigation was a fishing expedition. Don’t do that. This is a criminal investigation. Do your job, and then shut it down.”
If Mr. Mueller wanted to expand his investigation, Mr. Rosenstein told him, he should ask for additional authorities and resources.
But the special counsel built a staff — some inherited from the Justice Department and F.B.I., some of whom he hired — to investigate crimes, not threats to national security, which is the purview of counterintelligence investigations.
Simply investigating crimes, Mr. McCabe said, was a mismatched approach for a national security threat.
“It was first and foremost a counterintelligence case,” Mr. McCabe 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?”
Members of the special counsel team held early discussions led by the agent Peter Strzok about a counterintelligence investigation of the president. Those efforts fizzled when Mr. Strzok was removed from the inquiry three months later for sending text messages disparaging Mr. Trump.
Questions about the president’s ties to Russia dated to his presidential campaign.
Mr. Trump has sought to build a Trump Tower in Moscow for at least two decades, including during the campaign. His son Eric once said the Trump Organization relied on Russia for “all the funding we need” to purchase several golf courses in the United States. And the Senate report this month revealed the allegations of Mr. Trump’s potentially compromising encounters with women in Moscow in 1996 and 2013.
The F.B.I.’s mounting concerns about Mr. Trump reached a crescendo in the days after he fired Mr. Comey. Officials questioned whether Russia had leverage over the president and had dismissed the F.B.I. director to thwart any investigation that might reveal more. Their suspicions prompted agents including Mr. Strzok to open the counterintelligence inquiry.
The investigation was separate from the broader inquiry into the Trump campaign’s ties to Russia, code-named Crossfire Hurricane, that the bureau opened in the summer of 2016 to try to understand Russia’s operations to interfere in the election and whether Mr. Trump’s associates were conspiring with them.
The president and his allies have ramped up their attacks on that inquiry, misleadingly casting it as an illegitimate attempt by Democrats to spy on his campaign; independent reviews have found that investigators had sufficient reason to open it.
Mr. McCabe, convinced Mr. Trump would likely soon fire him, approved the opening of the inquiry into Mr. Trump, believing he was making it more difficult for anyone to interfere with or close the case without justifying doing so.
Mr. McCabe pushed Mr. Rosenstein to appoint a special counsel to conduct the investigation into Mr. Trump and the broader examination of Russia’s interference in the election. Two days later, Mr. Rosenstein appointed Mr. Mueller.
“It was the most enormous exhale of my life,” Mr. McCabe said. “I had been holding my breath” since the night Mr. Comey was fired, he added.
That day, Mr. Rosenstein joined Mr. McCabe while he briefed lawmakers about matters including the counterintelligence investigation and raised no objections.
The following day, Mr. McCabe briefed Mr. Mueller and his top deputies on the investigation into the president. But Mr. McCabe did not know that Mr. Rosenstein also gave his instruction to Mr. Mueller around that time to focus on whether crimes were committed.
Mr. Mueller later told Congress he did not conduct a counterintelligence investigation. The Democratic chairman of the House Intelligence Committee, Representative Adam B. Schiff of California, said in a memo released last week that he had reason to believe “that the F.B.I. Counterintelligence Division has not investigated counterintelligence risks arising from President Trump’s foreign financial ties.”
Mr. McCabe acknowledged that he underestimated Mr. Rosenstein’s willingness to conceal from him that he had curtailed the investigation. He remained at the F.B.I. for 10 months before being fired over displaying a lack of candor with internal watchdogs.
As Mr. McCabe left the bureau, he still believed Mr. Mueller was investigating Mr. Trump’s personal and financial ties to Russia.
This article is adapted from the book “Donald Trump v. The United States: Inside the Struggle to Stop a President,” being published on Tuesday by Random House.