From the moment Donald Trump secured the Republican nomination and then the presidency, national security officials under President Obama have shown themselves to be intense adversaries in public and behind the scenes.

In the latest development, special counsel Robert Mueller’s top-gun prosecutor, Andrew Weissmann, praised acting Attorney General Sally Yates, a Trump nemesis, for refusing a White House order to defend the president’s travel ban on Muslim-majority countries, according to internal emails.

Mr. Weissmann made it clear whose side he was on.

“I am so proud,” Mr. Weissmann wrote to Ms. Yates when he was the head of the Obama Justice Department’s criminal fraud division. “And in awe. Thank you so much. All my deepest respect.”

The U.S. Supreme Court this week approved Mr. Trump’s travel ban of targeted nations in a 7-2 ruling.

Mr. Weissmann, who as a private lawyer donated to Mr. Obama and to New York Gov. Andrew Cuomo, another Democrat, now is Mr. Mueller’s right-hand man. He oversaw the investigation of former Trump campaign manager Paul Manafort, including a pre-dawn FBI raid on his condo and an in-bed frisking of his wife.

The Weissmann emails and others from Obama political appointees praising Ms. Yates were unearthed in a Freedom of Information Act request by the conservative government watchdog Judicial Watch.

Mr. Trump fired Ms. Yates as she became a hero to Mr. Weissmann and other liberals.

The anti-Trump moves by Obama aides began in July 2016 during his campaign for the presidency.

Then-FBI Director James B. Comey began a criminal investigation of the Trump campaign, in whole or part, based on a dossier financed by the Democratic Party with an aim to destroy the Republican candidate. Its salacious and sometimes far-fetched scenarios of Russia-Trump collusion on the Russian hack of Democratic Party computers have not been confirmed publicly.

The top FBI investigator at that time was a “never Trump” advocate whom Mr. Mueller removed from his team last summer, The New York Times reported.

John O. Brennan, Mr. Obama’s CIA director and former campaign adviser, pushed the investigation during the campaign. He supplied Mr. Comey with the names of Russians with whom Trump associates had made any type of contact. Mr. Brennan testified to Congress that he provided the list of referrals without knowing what was discussed.

James R. Clapper, Mr. Obama’s director of national intelligence, has suggested that Mr. Trump is on the way out and calls him unfit for office.

“I really question his … fitness to be in this office,” Mr. Clapper told CNN after a fiery Trump speech in August. “And I also am beginning to wonder about his motivation for it. Maybe he is looking for a way out.”

Conservatives suspect all this has happened as Obama administration holdovers and former aides were working to sabotage the Trump administration.

‘A stealth coup’

Some news stories attributed to “former” government officials — read, Obama — have fallen into the “fake news” category. Journalists and Democrats are determined to show that Trump aides and Moscow collaborated.

A major New York Times story on Feb. 14 based in part on “former American officials” did much to fuel this narrative.

“Phone records and intercepted calls show that members of Donald J. Trump’s 2016 presidential campaign and other Trump associates had repeated contacts with senior Russian intelligence officials in the year before the election, according to four current and former American officials,” The Times story read.

Almost the entire story was wrong, according to Mr. Comey’s testimony before the Senate Select Committee on Intelligence four months later. In other words, there were no such “repeated contacts” with Russian intelligence.

Mr. Comey testified that he was so taken aback by the story that he immediately notified senior members of Congress that it was not true.

Another story that seemed to rise up from Obama holdovers was the narrative that Mr. Trump fired Mr. Comey in May because the FBI director had asked for more resources for a Russia-Trump investigation. Several senior Justice Department officials said no such request was made. Mr. Comey has not made that charge.

“Having experienced a change in administration while at the Pentagon in 2009, it’s not uncommon to see passive-aggressive behavior from a handful of outgoing folks,” said J.D. Gordon, a former Defense Department spokesman and Trump campaign national security adviser. “That said, based on the flood of leaks across the government, what we’re seeing today more closely resembles a stealth coup. Certainly nothing passive about it.”

Mr. Brennan has not shied away from depicting Mr. Trump as an awful president or disclosing his own role in driving the FBI to investigate Mr. Trump during the campaign.

“I wanted to make sure that every information and bit of intelligence that we had was shared with the [FBI] so that they could take it,” Mr. Brennan told the House Permanent Select Committee on Intelligence in May. “It was well beyond my mandate as director of CIA to follow on any of those leads that involved U.S. persons. But I made sure that anything that was involving U.S. persons, including anything involving the individuals involved in the Trump campaign, was shared with the bureau.

“I was aware of intelligence and information about contacts between Russian officials and U.S. persons that raised concerns in my mind about whether or not those individuals were cooperating with the Russians, either in a witting or unwitting fashion, and it served as the basis for the FBI investigation to determine whether such collusion [or] cooperation occurred,” the former CIA chief testified.

During the presidential transition, Rep. Peter T. King, New York Republican, became suspicious of Mr. Brennan’s behind-the-scenes maneuvers. He said on ABC News: “There should be an investigation of what the Russians did but also an investigation of John Brennan and the hit job he seems to be orchestrating against the president-elect.”

To date, there has been no public confirmation of Trump-Russia election collusion charges.

Any doubts that Mr. Obama’s CIA actively opposed Mr. Trump were perhaps dispelled by former acting Director Michael Morell. He endorsed Hillary Clinton in stark language in response to Mr. Trump’s comments as a candidate applauding Russian President Vladimir Putin.

“In the intelligence business, we would say that Mr. Putin had recruited Mr. Trump as an unwitting agent of the Russian Federation,” Mr. Morell said.

Curious Comey actions

Indeed, many Republicans expressed dismay at Mr. Trump’s praise of Mr. Putin, who has invaded eastern Ukraine, annexed the Crimean Peninsula and viewed NATO as an existential threat as he tries to destabilize Western democracies.

They also cringe at the president’s habitual Twitter feeds that often veer from policy and toward personal disputes with people in the media, Hollywood and sports.

Still, the machinations of Mr. Obama’s national security team seem to be unprecedented against a candidate, president-elect and president.

The FBI used the discredited dossier at least once to obtain a warrant to bug former Trump campaign volunteer Carter Page. Mr. Page said the collusion and bribery charges made by dossier writer Christopher Steele, a former British spy, are fiction. They ruined his investment business, he told the House intelligence committee.

“After over a year of false rhetoric and propaganda, it’s now refreshing that the real truth about what actually happened last year is starting to come to light,” Mr. Page told The Washington Times.

Other assaults on Mr. Trump: Mr. Comey elevated the dossier’s importance by briefing the president-elect at Trump Tower in New York City. Shortly thereafter, the briefing was leaked to CNN.

Mr. Comey wrote contemporaneous memos about his meetings with Mr. Trump and then leaked them to The New York Times via a middleman.

Then there is “unmasking,” the procedure in which senior national security figures may ask the intelligence community to disclose the names of Americans caught up in the eavesdropping of foreign agents.

Obama national security aides requested the unmasking of an undetermined number of Trump associates during the campaign, suggesting to Republicans that they were spying.

Obama people also have floated the talking point that the Trump campaign team violated the 1799 Logan Act by talking policy with Russian Ambassador Sergey I. Kislyak during the transition.

When The Washington Post wrote, based on top-secret intercepts, in February that retired Army Lt. Gen. Michael Flynn had spoken about sanctions against Moscow with Mr. Kislyak, the story brought up the obscure Logan Act as a possible violation.

Rarely if ever enforced, the Logan Act bars private citizens from urging foreign countries to oppose U.S. policies. The Trump transition, however, was not a private group but a government-funded agency.

That transition conversation with Mr. Kislyak proved fatal. Flynn pleaded guilty last week to providing false statements to the FBI when he denied discussing sanctions.

To Republicans, one of the most curious decisions by Mr. Comey was not to seize the Democratic Party computer servers hacked by two Russian cybercells. Instead, in one of the most important criminal investigations ever, Mr. Comey left it up to the private firm CrowdStrike to conduct a cybersecurity investigation and report to the FBI.

CrowdStrike employs former FBI agents and is funded in part by Google, a strong Democratic Party supporter.

If the Obama national security state declared war on Mr. Trump, it seems the FBI waged peace with Mrs. Clinton during the probe into her handling of classified material on her home email server during her tenure as secretary of state.

Mr. Comey, the Senate Judiciary Committee discovered, wrote an exoneration statement months before the investigation was concluded, even before interviewing the Democratic candidate.

CNN reported that Peter Strzok, the anti-Trump counterintelligence agent kicked off the Mueller probe, had a hand in changing the statement to lessen her culpability.

The draft wording was changed from “grossly negligent” — which is the legal definition of mishandling classified information — to “extremely careless,” the words Mr. Comey uttered at the exoneration press conference.

Mr. Comey downplayed the significance of Mrs. Clinton having her attorneys destroy about 30,000 emails with the app BleachBit. The FBI was able to reconstruct some those deleted emails, which showed they, too, contained classified information.

Mr. Mueller fired Mr. Strzok after the discovery of text messages between him and his lover, Lisa Page, a lawyer and aide to FBI Deputy Director Andrew McCabe, The Washington Post reported.

Mr. McCabe has come under criticism from Republicans for his own possible conflict of interest.

During the Clinton email investigation, his wife ran a losing campaign for the Virginia state Senate in 2015. She took a $467,000 donation from the political action committee of Virginia Gov. Terry McAuliffe, a Clinton family confidant.

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