How relations between White House and intelligence agencies crumbled in Donald Trump's first 100 days

The intelligence and security agencies in the US played a key role in Donald Trump’s election victory and they may yet be the ones who bring down this most extraordinary of presidents in recent American history.

Hillary Clinton could well have been in the White House now had it not been for James Comey. She was riding high when the FBI Director announced, just days before polling, that the investigation into the former Secretary of State’s use of her email account was being reopened.

Soon afterwards Mr Comey stated that nothing untoward had been discovered against Ms Clinton. But the damage had been done by then – her campaign lost momentum while that of Mr Trump solidified. While effectively sabotaging the Democrat campaign, Mr Comey helped Mr Trump’s by failing to reveal that an investigation into links between Mr Trump and Moscow, with evidence mounting, had been ongoing for months.

There were accusations that the FBI had tried to hide the Trump inquiry while focusing on Ms Clinton. Among those who claimed this to be the case was Christopher Steele, a former MI6 officer who produced a report on Mr Trump’s Kremlin links for the Democrats, and subsequently passed on incriminating information on Mr Trump and his associates to the FBI without any action being seemingly taken.

The New York office in particular appeared to be on a crusade against Ms Clinton. Some of its agents had a long working relationship with Rudy Giuliani, by then a member of the Trump campaign, since his days as public prosecutor and then Mayor of the city.

Two days before Mr Comey made his bombshell announcement about the Clinton reinvestigation, Mr Giuliani, part of the Trump team, talked about “a surprise or two you’re going to hear about in the next few days. We’ve got a couple of things up our sleeve that should turn things around”.

But Mr Trump cannot shake off the allegations that he was the “Muscovite Candidate”. Russia has been the dominant theme in the first 100 days of the presidency, raising fundamental questions even about his legitimacy in office. The Kremlin’s long reach, reads the charge sheet, ranges from cyber-attacks on Democratic Party computers to the funding of the Republican candidate’s election campaign.

There are now FBI and Congressional investigations into Mr Trump’s Moscow connections. The President has tried to dismiss them in his endless rambling tweets and tried to deflect attention with false claims such as that he had been wiretapped on the orders of President Obama. There have, in addition, been attempts to stop important witnesses from testifying. But the inquiries continue.

Mr Trump is now at loggerheads with the intelligence community. The antipathy of many of them towards him has been hardened by episodes such as his behaviour when he visited the CIA headquarters. Standing in front of the Memorial Wall – a place of reverence in the Agency – Mr Trump boasted about the fictitious size of his inaugural crowd and his own intellect: “And then they say, ‘Is Donald Trump an intellectual?’ Trust me, I’m like a smart person.” Former CIA director John Brennan let it be known that he was “deeply saddened and angered at Donald Trump’s despicable display of self-aggrandisement in front of CIA’s Memorial Wall of agency heroes. Mr Trump should be ashamed of himself”.

Meanwhile, even senior figures in the Trump administration, including Defence Secretary James Mattis and Secretary of State Rex Tillerson, have acknowledged Moscow’s interference in the US election.

Mr Tillerson’s own Kremlin connections have been questioned. He forged close ties with Russia during his 40 years of work for Exxon Mobil, and he worked on projects with the Russian state-owned oil company Rosneft. He is said to be close to its head Igor Sechin, a close confidant of Vladimir Putin. In 2013 the Kremlin awarded him the Order of Friendship.

Senior Republicans like Senator John McCain had questioned whether Mr Tillerson was a fit person for his job with his close Russia ties. There have been questions, in particular, about Mr Sechin, who was named in the Steele report as one of the senior Kremlin officials who had met members of the Trump team before the election.

There are, however, others in the team who are under more intense scrutiny than Mr Tillerson. There has already been a high-profile casualty, Lieutenant General Michael Flynn, who resigned as Mr Trump’s national security advisor after just three weeks over his contacts with the Russian ambassador to the US.

Lt Gen Flynn was accused of lying to Vice President Mike Pence over his insistence that he had not discussed against Russia with Sergey Kislyak. It transpired later that he was under investigation by the Pentagon for allegedly accepting Russian payment during trips to Moscow. He was to go on to admit working as a “foreign agent”, receiving money while representing the Turkish government in a dispute with the United States.

Lt Gen Flynn resigned on the same day Barack Obama announced sanctions against Russia for attempting to influence the presidential election, and hours after Mr Trump had expressed “full confidence” in his National Security Advisor.

Lt Gen Flynn has subsequently offered to appear before the Senate Intelligence Committee in return for immunity from prosecution – an offer the Committee has so far rejected.

Paul Manafort’s resignation as Mr Trump’s campaign manager came before the election. He had filled the same role with Viktor Yanukovych, Ukraine’s former president, an ally of Mr Putin who is now in exile in Russia after being overthrown in the Maidan protests. It was money he received in his Ukrainian job which led to him leaving the Trump team, although he appears to have remained an influential voice behind the scenes.

There are now fresh allegations that Mr Manafort received vast sums in “suspicious payments” from Mr Yanukovych. Prosecutors in Kiev want to question Mr Manafort and say they have requested the assistance of Mr Comey in doing so. It is seen as a sign of the Trump administration’s nervousness about what may unfold that it appears to be trying to distance itself from Mr Manafort. In a recent briefing to journalists, the White House spokesman Sean Spicer brought up Mr Manafort’s name unprompted, and claimed, to general incredulity, that “he played a very limited role, very limited amount of time” in the presidential campaign.

The same kind of damage limitation is being tried with Carter Page, who Mr Trump had formerly described as a foreign policy advisor and Mr Spicer now wants to stress was “not really a major part of the campaign”.

According to Mr Steele and others who have provided information to the FBI, Mr Page had discussed intelligence being held by Russia on Ms Clinton with a senior Kremlin official and the issue of ending sanctions against Moscow with Mr Sechin. He also allegedly met a Russian intelligence operative, Victor Podobny, in 2013 and offered to provide him with documents about the energy industry.

The FBI obtained a warrant under the Federal Intelligence Surveillance Act (FISA) to carry out surveillance on Mr Page as the suspected “agent of a foreign power”. Mr Page says “that his civil rights have been violated” and he is the “real victim of a conspiracy”.

As investigations continue into Mr Trump, “conspiracy” is a recurring theme among his supporters. They warn of a “coup” being planned by the “deep state” of the establishment and the intelligence services to unseat an elected President.

Mr Trump’s many enemies, meanwhile, hope that the investigations will lead to eventual impeachment of the President they loathe. What the intelligence and security agencies uncover, or fail to do, in the weeks and months ahead will shape the fate of the Trump presidency.