Editor's Note: (Laura Coates is a CNN legal analyst. She is a former assistant US attorney for the District of Columbia and trial attorney in the Civil Rights Division of the Department of Justice. She is the host of the daily "Laura Coates Show" on SiriusXM. Follow her @thelauracoates. The views expressed are her own.)

(CNN) An old adage says, "I didn't come this far to only come this far." The saying is quite apropos when it comes to federal prosecutors' offering a plea for lying.

It may appear at first blush that former national security adviser Michael Flynn's guilty plea on one charge of lying to federal agents is a colossal waste of resources by special counsel Robert Mueller, and proof of a media-driven hyperbolic tale of collusion. But, in reality, the plea is a clear indication that the cloud of suspicion that has plagued the Trump White House just started to rain on the Oval Office.

Laura Coates

A plea is a compromise between prosecutors and a defendant where the defendant agrees to provide certain information in exchange for some benefit. The defendant proffers specific testimony to the prosecution. In exchange for that testimony, the prosecutors will agree not to charge the defendant with any crime, limit the severity of the charges or agree to a favorable sentencing recommendation.

But prosecutors do not negotiate in the name of altruism; they require some tangible benefit in return. In assessing the potential benefit, prosecutors consider the value of the information, their ability to glean the information from any other source, the nature of the available charges and whether a favorable plea would preclude them from imposing the highest penalty on the worst actor.

To invoke the "big fish" analogy, a prosecutor has no interest in letting the biggest fish off the hook. Instead, they use plea offers to hook smaller fish as bait.

Other than the President himself, the national security adviser to the President of the United States would normally be the quintessential Moby Dick. But, ironically, his brief 24-day tenure immediately downgraded him to the role of bait.

If the investigation uncovers far more substantial allegations against any members of the Trump campaign or administration, Flynn's resignation may ultimately be his saving grace.

Although relegated to bait, Michael Flynn is no coffee boy, as officials have called George Papadopoulos, the former Trump campaign adviser who pleaded guilty this summer to lying to federal agents. Still, Ty Cobb's statement regarding Michael Flynn seeks to use the brevity of Flynn's brief tenure to downplay Flynn's importance while praising the Trump administration for proactively calling for his resignation.

But Cobb's statement is a thinly veiled attempt to distance President Trump's inner circle from Michael Flynn and hide their presumed anxiety about what incriminating information Flynn has agreed to provide in exchange for his plea.

Frankly, such anxiety is warranted. The charge to which Flynn has pleaded guilty confirms that Robert Mueller is disbelieving and intolerant of the selective amnesia that has seemingly afflicted campaign, transition team or administration officials like Attorney General Jeff Sessions and President Trump's son-in-law, Jared Kushner, following their contact with Sergey Kislyak.

The government's statement of facts in support of Flynn's plea suggests that he informed a senior transition official of his communications with Kislyak, and was perhaps even directed by that person. Reporting suggests that that official is the President's son in-law, Jared Kushner.

President Trump and top White House aides have repeatedly denied that Trump has used any untoward influence to end investigations into Russia, and on Wednesday, Jared Kushner's lawyer told CNN, "Mr. Kushner has voluntarily cooperated with all relevant inquiries and will continue to do so."

If that is true, in an investigation that lends itself to "bigger fish" analogies, perhaps the more appropriate analogy is that of Matryoshka, Russian nesting dolls. With each guilty plea, another doll of bravado is opened, revealing a smaller concentration of potent power. Who will be left standing in the center is a question for Mueller.