Washington (CNN) Michael Flynn's downfall Friday exacerbated grave legal and political risks that represent the most serious threat to any administration for at least 40 years, and could eventually imperil the Trump presidency itself.

The plea deal cut by the fired national security adviser with Special Counsel Robert Mueller undermines much of what the White House has said about the Russia controversy engulfing the presidency.

It means there is now no credible way for President Donald Trump to claim the Russia investigation is a hoax, made up, fake news or a witch hunt.

It raises questions about who higher up the chain of command in Trump's orbit -- possibly even including the President himself -- is in Mueller's sights after he agreed to what appears to be a fairly favorable deal with the retired general

New details about Flynn's conversations with then Russian ambassador to the US Sergey Kislyak and involvement in a controversy at the United Nations involving Israel meanwhile raise the possibility that the nascent Trump administration tried to seize control of the levers of state power before it was inaugurated.

Above all, Flynn's plight ensures the dark Russia cloud that has overshadowed everything the administration has done for 10 months is unlikely to lift soon -- and may well thicken.

Legal dimension

Friday's staggering developments did not prove that Trump or other senior aides colluded with Russia to throw the 2016 election -- the centerpiece of Mueller's assignment.

But they make clear that the Mueller probe is marching deep inside the President's tightest inner circle and is threatening officials and family members it would be impossible for him to dismiss as marginal, junior players.

"Not many months ago, the President liked to call this 'fake news' and a fake investigation and a 'witch hunt.' As of today there is no fake investigation, there is no fake news, there is no witch hunt," former US Attorney Michael Moore told CNN.

"Mike Flynn, a high-ranking member of the Trump administration, in charge of our national security, has now come in and admitted the allegations are in fact true," Moore said.

Mueller's decision to charge Flynn with one count of lying to the FBI on four separate occasions is a relatively limited move that suggests he expects to get significant and sweeping information in return.

The fact that a former national security adviser -- one of the most senior members of the government -- is not Mueller's primary target, as evidenced by the plea deal, suggests Flynn is being used as bait for a bigger fish.

It may be a sign Mueller does not intend to end his investigation merely by indicting people on the charges lying under oath, as some previous independent prosecutors of government wrongdoing have done.

"Normally, somebody who is a national security adviser would be one hell of a Moby Dick ... he is now bait," said CNN legal analyst Laura Coates.

The charges that Mueller did choose to lay against Flynn are also revealing.

He specifically chose lies linked to Flynn's conversations with Kislyak about US sanctions against Russia and a UN Security Council vote on Israeli settlements at the tail end of the Obama administration. That is potentially significant because it could widen the circle of the Mueller investigation to people around Trump who were involved in those issues -- possibly including Trump's son-in-law, Jared Kushner, and his son Donald Trump Jr.

CNN reported Friday that Kushner -- a top Trump political adviser was the "very senior adviser" who directed Flynn to contact the Russians about the Security Council vote.

JUST WATCHED Comey goes biblical after Flynn plea Replay More Videos ... MUST WATCH Comey goes biblical after Flynn plea 01:42

"The four lies that he picked tell you something very important, that this is an ongoing investigation that implicates a lot of people in the Trump inner circle," said former federal prosecutor Michael Zeldin. "This portends a lot of bad news for a lot of people for a lot of reasons."

In a prosecutor statement released Friday, it was revealed that Flynn called senior transition officials on December 29 last year to discuss his conversations with Kislyak and that there were multiple conversations with the transition team while he was talking with the Russian envoy about sanctions.

The statement did not identify those officials but it sparked intense speculation in Washington about whether Trump was in any way involved in directing Flynn's role in those conversations, or was aware of their content.

"This shows a Trump associate negotiating with the Russians against US policy and interests before Donald Trump took office and after it was announced that Russia had interfered in our election," said Democratic Sen. Dianne Feinstein in a statement. "That's a stunning revelation and could be a violation of the Logan Act, which forbids unauthorized US citizens from negotiating with a foreign power."

Flynn's admission that he was in close coordination with senior transition team officials also undermines a possible line of defense from the administration -- that he was freelancing and acting on his own volition in his contacts with Kislyak. It also potentially exposes many other key figures who were in Trump's transition and followed him into the White House to Mueller's probe.

Implications

The focus on Russia sanctions is also potentially significant.

US intelligence estimates assess that a Russian effort to meddle in the election was largely motivated by a desire to promote the lifting of US sanctions against leading members of President Vladimir Putin's inner circle that also had a damaging impact on the Russian economy.

Flynn's downfall is also a weightier legal threat to the White House than the previous indictments of former campaign manager Paul Manafort and his associate Rick Gates in October. Those initial Mueller targets were largely indicted for business and lobbying activities and on financial charges not directly linked to the Trump campaign or his transition and presidency.

It was therefore possible for Trump's team to argue that they were peripheral not just to the White House but also to the central question of whether the President or associates colluded with Russia to meddle in the election.

Such a case cannot be made about Flynn, since his charges relate directly to activity during the transition and he has admitted lying to the FBI while actually serving as national security adviser.

Similarly he cannot be dismissed as a minor player, or a "coffee boy," as former Trump foreign policy aide George Papadopoulos was when he entered a plea deal with Mueller in October.

Flynn was the President's constant companion during the campaign. The President asked the former FBI chief to go easy on Flynn before he fired Comey. And Flynn was the man responsible for keeping, and acting upon, the nation's most closely guarded national security secrets.

The legal issues raised for the President and his associates by news of Flynn's plea deal that exploded on Washington may actually pale beside the political dimensions of the now more severe threat posed by the Russia probe.

Despite protestations to the contrary, the White House is under siege and its impact on the political effectiveness of the administration cannot be discounted.

Disclosures about Flynn's behavior only deepen the central intrigue of the the entire episode: Why have the President, his family and aides repeatedly lied about the extent and nature of their contacts with Russians?

Spin doctors

The shocking developments were reflected in the unconvincing early spin from Trump's defenders.

A source close to the President told CNN's Gloria Borger that everybody lies in Washington.

A person familiar with the mood in the West Wing told CNN's Sara Murray that people in the building were "very happy" because the charges were about making false statements and not improper actions.

Such a view, however, ignores the potentially sweeping implications of Flynn's cooperation with Mueller.

The President's lawyer Ty Cobb issued a statement noting that the charges against Flynn involved the same false statements that led to his firing, after he lied to Vice President Mike Pence, about his Kislyak calls in February.

Cobb also attempted some political damage control, pointing out that Flynn served for only 25 days as national security adviser and was a former Obama administration official. But a senior aide to the former president noted to CNN's Jim Acosta that Obama had fired Flynn as the head of the Defense Intelligence Agency and advised Trump not to hire him.

So far, there has been no reaction to the fall of his former close aide from Trump himself. But the President has spent months using his Twitter feed and public events to malign the Russian investigation and incite his followers against it seemingly in an attempt to delegitimize its eventual conclusions.

JUST WATCHED Flynn pleads guilty to lying to FBI Replay More Videos ... MUST WATCH Flynn pleads guilty to lying to FBI 14:34

The impact on Trump's temperament and mood -- at a time of a dangerous nuclear crisis involving North Korea -- and the potential of the latest Russia revelations to further distract him -- will be even more closely watched now.

The sheer magnitude of Friday's events left Trump's defenders within his party with yet another infuriating distraction in their relationship with the President.

Senate Intelligence Chairman Richard Burr of North Carolina, who is leading his own probe into the Russia issue, refused multiple requests by CNN's Manu Raju to comment on Friday's bombshell developments.

In many ways that's the story of the Trump presidency itself -- everything has been overshadowed by Russia.