By Elie Honig

(CNN) -- Special counsel Robert Mueller informed a federal judge on Monday that Paul Manafort's cooperation deal has imploded because of Manafort's seemingly congenital inability to tell the truth.

On the surface, Manafort's failed cooperation appears to be a setback for Mueller and a bullet dodged for President Donald Trump and administration insiders. But Mueller's ability to see through Manafort's lies and rip up the cooperation agreement bespeaks a deeper strength. By Monday's court filing, Mueller effectively declared: I have enough evidence to know Manafort is lying to protect others, and I don't need his half-baked cooperation to prove my case against them.

As a federal prosecutor, I dealt with dozens of cooperators, including gun and drug traffickers, corrupt public officials, mafia leaders and murderers. I spent countless hours interviewing (or "proffering," in the lingo) potential cooperators and assessing whether they were being honest and forthcoming.

Federal cooperation is an all-or-nothing proposition; the cooperator must tell the prosecutor everything he knows about any crime that he or anybody else has committed. There are no half-measures. The cooperator cannot withhold incriminating information about certain people he wishes to protect. This selectivity is the most common cause of failed cooperation, and it appears to be Manafort's undoing here.

Whatever the particular reason for the breakdown, there is no avoiding the conclusion that, had Manafort cooperated fully and truthfully, he likely could have done serious damage to high-ranking administration and campaign officials, including potentially Trump himself. Manafort spent five months as Trump's campaign chair, and he attended inner-circle meetings, including the infamous June 2016 Trump Tower sit-down between Donald Trump Jr., Jared Kushner and a group of Russians who were said to have offered to provide dirt on Hillary Clinton to the Trump campaign.

Had Manafort come clean, as required by his cooperation agreement, he could have walked Mueller into the inner sanctum of the Trump campaign during the key months leading up to the 2016 election, during which Russian intelligence agents hacked and disseminated the emails of Hillary Clinton and the DNC in an effort to undermine Clinton and help Trump's campaign. Doubtless, some within the Trump administration breathed sighs of relief when they learned that Manafort's cooperation had tanked.

At the same time, the very fact that Mueller saw through Manafort's lies -- and appears ready to prove to Manafort's sentencing judge that Manafort lied -- is a subtle but powerful show of strength.

When a prosecutor pulls the plug on a cooperator because that cooperator lies, it typically happens not merely because the prosecutor senses in his gut that the cooperator is lying. More often, the prosecutor knows for a fact that the cooperator is lying because the prosecutor has hard evidence to prove the truth of the matter.

Here, we know Mueller has the goods on whatever Manafort lied about -- and whoever Manafort felt a need to protect -- because he told the judge that he "will file a detailed sentencing submission to the Probation Department and the Court in advance of sentencing that sets forth the nature of the defendant's crimes and lies, including those after signing the plea agreement." Translation: Manafort lied, I know it, and I'll prove it at his sentencing if necessary. That should cause serious concern to whoever Manafort sought to protect by lying to federal prosecutors during his proffers.

As for Manafort himself, Anderson Cooper said it best: How frickin' stupid is this guy? Manafort, now 69 years old, already faced a sentence likely to keep him behind bars for most or all of his remaining life following his August trial conviction on eight crimes, including bank fraud and tax evasion. Manafort then pleaded guilty to additional crimes under a cooperation agreement, which provided him with one potential out: If he cooperated successfully, he could earn a "5K letter" from Mueller detailing Manafort's cooperation. (A 5K letter -- named after the relevant provision of the federal sentencing guidelines, section 5K1.1 -- is a letter from the prosecutor informing the judge of the details of the defendant's cooperation.)

I've written many 5K letters, and I know that they can result in drastically reduced sentences. Now, however, Manafort has the worst of all worlds. He has been convicted at trial, he has pleaded guilty to additional crimes, he has broken his own cooperation agreement by lying federal prosecutors, and he has no chance at a 5K letter. Manafort paddled far upstream and now he has thrown his oar into the rapids.

So, why then would Manafort endanger himself by lying to Mueller? I see two possible explanations. One, perhaps Manafort is simply an arrogant, congenital liar. The trial evidence proved that Manafort believed he could spin a web of lies and get away with them. He got caught lying to banks and the IRS, and now, unsurprisingly, he has been caught by Mueller. Some cooperators understand that they are best served by telling the truth, for better or worse; others play games with prosecutors and end up getting burned.

Two, Manafort may be playing for a longshot pardon or commutation from Trump. It already has been reported, before Manafort's trial conviction and cooperation plea, that Trump at least discussed the possibility of pardoning Manafort.

Perhaps Manafort has determined on his own that his best chance to earn a pardon is to walk away from Mueller (though it is unclear why Manafort would curry favor with Trump by cooperating with Mueller and then lying; Manafort could have sent the same message of loyalty by refusing to cooperate at all in the first place). Or it is possible -- unproven at this point, but possible, given the chain of events -- that word somehow got to Manafort that, if he scuttled his cooperation with Mueller, he would be rewarded with a pardon. If that happened, then anybody who put the word out, or helped get it to Manafort, would face potential charges for obstruction of justice.

The failure of Manafort's cooperation at first glance seems like a setback for Mueller. But the fact that Mueller was able to call out Manafort's lies suggests he has plenty of evidence in hand to go after whoever Manafort sought to protect.