For many, Friday’s arrest of Roger Stone, the veteran political trickster and longtime adviser to Donald Trump, was a sign that the special counsel investigation into Russian electoral interference is entering its final phase. Yet there were also several indications that the probe may not be as near its conclusion as many observers assume — and that the true target of Friday’s F.B.I. actions was not Mr. Stone himself, but his electronic devices.

Mr. Stone’s early-morning arrest at his Florida home unsurprisingly dominated coverage, but reports also noted that federal agents were “seen carting hard drives and other evidence from Mr. Stone’s apartment in Harlem, and his recording studio in South Florida was also raided.” The F.B.I., in other words, was executing search warrants, not just arrest warrants. Even the timing and manner of Mr. Stone’s arrest — at the absolute earliest moment allowed under federal rules of criminal procedure without persuading a judge to authorize an exceptional nighttime raid — suggests a concern with preventing destruction of evidence: Otherwise it would make little sense to send a dozen agents to arrest a man in his 60s before sunrise.

The indictment itself — which charges Mr. Stone with witness tampering, obstruction of justice and false statements to Congress — takes little imagination to translate into a search warrant application, and also hints at what Robert Mueller might be looking for. In describing the lies it alleges Mr. Stone told a House committee, the document places great emphasis on Mr. Stone’s denial that he had any written communications with two associates — associates with whom he had, in fact, regularly exchanged emails and text messages. That’s precisely the sort of behavior one might focus on in seeking to convince a recalcitrant judge that an investigative target could not be trusted to turn over documents in response to a subpoena, requiring the more intrusive step of seizing Mr. Stone’s devices directly.

Of course, as the indictment also makes clear, the special counsel has already managed to get its hands on plenty of Mr. Stone’s communications by other means — but one seeming exception jumps out. In a text exchange between Mr. Stone and a “supporter involved with the Trump Campaign,” Mr. Mueller pointedly quotes Mr. Stone’s request to “talk on a secure line — got WhatsApp?” There the direct quotes abruptly end, and the indictment instead paraphrases what Mr. Stone “subsequently told the supporter.” Though it’s not directly relevant to his alleged false statements, the special counsel is taking pains to establish that Mr. Stone made a habit of moving sensitive conversations to encrypted messaging platforms like WhatsApp — meaning that, unlike ordinary emails, the messages could not be obtained directly from the service provider.

The clear implication is that any truly incriminating communications would have been conducted in encrypted form — and thus could be obtained only directly from Mr. Stone’s own phones and laptops. And while Mr. Stone likely has limited value as a cooperating witness — it’s hard to put someone on the stand after charging them with lying to obstruct justice — the charges against him provide leverage in the event his cooperation is needed to unlock those devices by supplying a cryptographic passphrase.

Of course, Mr. Mueller is likely interested in his communications with Trump campaign officials, but the detailed charges filed against the Russian hackers alleged to have broken into the Democratic National Committee’s servers also show the special counsel’s keen interest in Mr. Stone’s communications with the hacker “Guccifer 2.0,” an identity said to have been used as a front for the Russian intruders. By Mr. Stone’s own admission, he had a brief exchange with “Guccifer” via private Twitter messages. On Mr. Stone’s account, Guccifer enthusiastically offered his assistance — at the same time we now know Mr. Stone was vigorously pursuing advance knowledge of what other embarrassing material stolen from Mr. Trump’s opponents might soon be released — and Mr. Stone failed to even dignify the offer with a reply. With no easy way of getting hold of “Guccifer’s” cellphone, searching Mr. Stone’s devices might be the only reliable way for the special counsel to discover whether the conversation in fact continued on a more “secure line.”

Yet if Mr. Mueller is indeed less interested in Mr. Stone than the potential evidence on his phones and computers, the conventional wisdom that the special counsel probe is wrapping up — and could issue a final report as soon as next month — seems awfully implausible. Digital forensics takes time, and a single device could easily hold many thousands of messages to sift through. And if this really is the first time Mr. Mueller’s office is seeing the most sensitive communications from a key figure like Mr. Stone, it’s likely they’ll come away with new leads to follow and new questions to pose to other witnesses.

We may ultimately look back on Mr. Stone’s arrest not as the beginning of the special counsel’s endgame, but the point when the investigation began to really heat up.

Julian Sanchez is a senior fellow at the Cato Institute.

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