The arrest and indictment of a former senior FBI counterintelligence agent, Charles McGonigal, has reopened an embarrassing subject for the FBI and the Department of Justice: Oleg Deripaska.

Mr. Deripaska is a billionaire ally of Russia’s president, Vladimir Putin. He made his fortune after the dissolution of the Soviet Union by taking over his country’s aluminum industry. He is a central character in the Democratic Party’s narrative about Russian collusion.

The Senate Intelligence Committee in 2020 accused Mr. Deripaska of coordinating influence operations on behalf of the Kremlin throughout the world. His one-time business relationship with President Trump’s former campaign manager, Paul Manafort, presented a grave threat to the country, according to the committee.

Yet an FBI agent who helped to investigate the alleged Russian collusion of Mr. Trump’s campaign is now accused by his former colleagues of working for the same guy who was running an off the books information war for Moscow.  

Now this may seem like a remarkable betrayal, worthy of a spy thriller. A closer look at Mr. Deripaska’s relationship with the FBI, though, shows that the bureau misjudged the villain of Russiagate for years.

Despite warnings from the Department of State in the 2000s, the FBI sought out Mr. Deripaska’s cooperation when Robert Mueller led the bureau between 2001 and 2013. Mr. Mueller would of course go on to be the special counsel who investigated and could not find evidence of the original Russia collusion plot.

In 2009, the FBI persuaded Mr. Deripaska to spend millions of his own dollars on an operation to find a former FBI agent who went missing in Iran in 2007 while on an assignment for the CIA, Robert Levinson.

Between 2014 and 2016, the FBI tried to entice Mr. Deripaska to turn on President Putin. The bureau was rebuffed. In an embarrassing episode in 2016, agents showed up at the oligarch’s home in New York and asked whether Mr. Manafort was part of a Russian plot to influence the election. Mr. Deripaska denied the allegation and then reported the entreaty to the Kremlin.

In this same period, a former British spy contracted by Hillary Clinton’s campaign in 2016 to produce the now discredited dossier that alleged Mr. Trump’s collusion with Russia, Christopher Steele, was also working for Mr. Deripaska. He had a contract to help find and recover debts owed to the oligarch by Mr. Manafort.

Mr. Steele’s alleged research of course was seized upon by senior FBI leaders in the run-up to the 2016 election. His debunked “research” was submitted to the secret surveillance court to obtain a spy warrant for an adviser to Mr. Trump’s campaign, Carter Page.

Mr. McGonigal’s own career is also a black eye for the bureau. He was an ally of the FBI director who Mr. Trump fired in 2017, James Comey, who promoted him to his last job at the bureau in 2016 as the chief counterintelligence officer for the FBI’s New York field office.

On the day Mr. Comey was fired by Mr. Trump in 2017, Mr. McGonigal told an event that he was one of the “most loved leaders” in the bureau’s history.

Mr. McGonigal will have his day in court. His lawyer has said he intends to fight the charges and looks forward to discovery. So it’s important to read the unsealed indictments for now as allegations.

That said, the FBI misjudged Mr. Deripaska for years. Until 2017, the FBI believed that he was a man with whom they could do business. Even the author of the Trump-Russia dossier was willing to work for him. If the indictment is correct, so was one of the bureau’s most senior counterintelligence agents.