Michael Flynn, former national security adviser, has admitted lying to the FBI and cut a plea deal. Credit:Bloomberg Mueller was appointed to investigate "any links and/or co-ordination between Russian government and individuals associated with the campaign of President Donald Trump, and any matters that arose or may arise directly from the investigation". There was always smoke. Mueller's recent moves suggest he believes he has found fire. How did we get here? A month before Trump's shock victory in November last year American intelligence agencies declared they believed Russia was seeking to derail Hillary Clinton's campaign. Clinton and Vladimir Putin had loathed one another since Clinton's time as Secretary of State during Barack Obama's first term, and Putin believed that a Clinton administration would be a far tougher counterpart than Trump.

On October 7 the Office of the Director of National Intelligence and the Department of Homeland Security jointly stated that US intelligence believed Russia had directed the hacking of Democratic National Committee's email system during the election. Damaging emails were subsequently released via Wikileaks at key points during the campaign. Trump remains an unpopular president who commands real support in the Republican base. Credit:AP On October 31 Obama called Putin and told him to stop his interference. With investigations continuing by the FBI, intelligence agencies and Congressional committees about apparent financial ties between Trump associates and the Kremlin, Trump sacked the FBI director Robert Comey on May 9. There was always smoke. Mueller's recent moves suggest he believes he has found fire. Credit:AP

The New York Times later reported that the following day Trump told Russian officials visiting the Oval Office, "I just fired the head of the FBI. He was crazy, a real nut job,I faced great pressure because of Russia. That's taken off." On May 11 Trump told NBC, "When I decided to [fire Comey], I said to myself, I said you know, this Russia thing with Trump and Russia is a made up story." Paul Manafort, accompanied by his lawyers, arrives at federal court in Washington on November 2. Credit:AP On May 17 Mueller was appointed Special Counsel for the Justice Department to lead the collusion investigation. Key moments

The first sign that he was making concrete advances came on October 30 with news of charges being laid against two key figures. One was Paul Manafort, a political gun-for-hire who had made a fortune consulting for the ousted pro-Putin Yanukovych government in Ukraine before being appointed Trump's campaign manager. The other was his business partner, Rick Gates. They surrendered to the FBI on October 30 and have pleaded not guilty to charges including conspiracy against the United States, conspiracy to launder money and lying to the FBI. Even more chilling for Trump's White House was the revelation at the same time that months earlier, on July 27, George Papadopoulos, a former foreign policy adviser to Donald Trump, had secretly pleaded guilty to lying to the FBI. In the intervening period he had acted as a so-called "proactive witness" – effectively acting as a spy for the investigation in return for leniency. There have been other extraordinary revelations. In May the Washington Post revealed that Trump's son-in-law and senior adviser, Jared Kushner, and Russia's ambassador to Washington, Sergey Kislyak, discussed the possibility of setting up a secret and secure communications channel between Trump's transition team and the Kremlin, using Russian diplomatic facilities in an apparent move to shield their pre-inauguration discussions from monitoring.

A fortnight ago Kislyak said during an interview with Russian media that he could not name all the Trump officials he has spoken with because it would take too long. Where Flynn fits in News that Flynn has pleaded guilty to lying to the FBI and, in return for leniency, agreed to co-operate with the investigation is the most serious development yet. Flynn is a former general who became central to Trump's campaign, a hyper-partisan who led chants of "Lock Her Up!" about Hillary Clinton during Trump's boisterous nomination convention last year and railed against the dangers of Islam. He had also had his own Russian ties, sitting next to Putin and delivering a foreign policy speech during a function hosted by the Kremlin-controlled media outlet RT in 2015, for which he was paid $45,000. On January 20 he was appointed to be Trump's National Security Adviser, one of the most senior roles in administration.

He resigned just weeks later after it was revealed he had lied to Vice-President Mike Pence about his dealings with Kislyak. Investigators will now be asking him if Trump or another official instructed him to contact the Russians, and if so, to what end. "Those in Flynn's orbit should be terrified by today's development," Stephen A. Miller, a lawyer and former federal prosecutor who has specialised in corruption cases told the Washington Post. "A structural plea like this is more ominous for President Trump and others than one where the book was thrown at Flynn. Today's deal signals that Flynn is being rewarded for co-operation deemed highly valuable by Mueller." Mueller's footsteps When Mueller was appointed as Special Counsel even Trump's allies noted that he was the right man for the job. Mueller is a combat veteran who was decorated for his heroism in Vietnam. He went on to become an FBI agent and then FBI director, famed for his impartiality. He was also the man who sharpened FBI's focus on counter-espionage.

The path he has taken in this investigation resembles one that he might once have led into organised crime. He started at the outside of the organisation, he secured leverage over foot soldiers and turn them into informants, moving higher up the chain at each point. Having flipped Flynn there is not much higher he can go. Only three names spring to mind – Jared Kushner, Donald Trump Jr, Donald Trump. So far the White House is playing down Flynn's admission. "Nothing about the guilty plea or the charge implicates anyone other than Mr. Flynn," said Trump's lawyer Ty Cobb in a statement. "The conclusion of this phase of the Special Counsel's work demonstrates again that the Special Counsel is moving with all deliberate speed and clears the way for a prompt and reasonable conclusion."

This is optimistic at best. If Mueller believed his investigation ended with Flynn, he would have thrown the book at him rather than cut a deal with him for even more information. Where to next? It could be that the White House is right, that Mueller's investigation will end before Christmas without more revelations. But the signs are that Mueller believes people even closer to the president – or the president himself – broke the law in colluding with Russia and in seeking to derail the subsequent investigation. These would be impeachable offences, but impeachment is a political rather than a judicial process, once that would need to conducted by a Republican-controlled congress.

Loading So far Trump remains an unpopular president who commands real support in the Republican base, and as a result congressional Republicans have so far proved unwilling to challenge him. And as media focuses on this staggering investigation, Republicans are focused on passing tax cuts.