Read: It was all in plain sight

Thanks to the Mueller inquiry, individuals associated with this election scandal are beginning to face justice. But also thanks to the Mueller inquiry, the nation remains as vulnerable as ever to the consequences of the scandal: a president beholden to a hostile foreign power.

When the Mueller probe was initiated almost two years ago, I worried here at The Atlantic:

A special prosecutor could wrap the investigation of the Trump-Russia matter in secrecy for months and years—and ultimately fail to answer any of the important questions demanding answers.

I worried because:

A special prosecutor … seeks crimes. The criminal law is a heavy tool, and for that reason it is thickly encased in protections for accused persons. The most important protection from the point of view of the Trump-Russia matter is the rule of silence. A prosecutor investigating a crime can often discover non-criminal bad actions by the people he is investigating. If those bad actions do not amount to crimes, the prosecutor is supposed to look away.

Today’s Stone indictment pounds home that warning. Robert Mueller does not have a record of bringing frivolous charges. If Mueller convicts, Stone will then face a lengthy term in prison, perhaps alongside his former lobbying-firm partner, Paul Manafort. Mueller is likely moving now to the next step in the chain, and more indictments will ensue.

Read: Why Democrats have suddenly started talking about impeachment

But how does this backward-looking justice serve the country now? The Mueller investigation has impressively suppressed all leaks. It has spoken only to slap down news reports it regards as incorrect and inflammatory, such as the BuzzFeed report last week that President Donald Trump had directly counseled his former lawyer Michael Cohen to lie to Congress. The result of this praiseworthy discretion is that the main thing the country has to worry about—Trump’s obligations to Putin—remains wrapped in official silence. The prosecutorial mission is being carried out with textbook professionalism. Meanwhile, we are losing sight of the underlying purpose of the mission—to protect the country from a potentially disloyal president.

Through the election and to this day, the Russians have held damaging information about Trump, information that is only now being confirmed to Americans. In October 2016, it was an obvious inference that the Trump campaign was working with WikiLeaks. Now that obvious inference forms the basis of an indictment.

Many other inferences could be drawn today, but there is not yet public evidence to support them, and they are not yet lodged as formal criminal charges: financial connections between Trump and Russia, the sharing of operational campaign information, and other terrible possibilities, too.