Special counsel Robert S. Mueller III leaves Capitol Hill in June 2017. (Andrew Harnik/AP)

THIS WEEK brought tantalizing hints about special counsel Robert S. Mueller III’s Russia investigation, prompting rampant speculation about the inquiry’s direction. It remains unclear whether these revelations will add up to a case that President Trump colluded with the Russians to sway the 2016 presidential election. Yet what they do prove is that there are more than enough troubling questions and shady Trump associates to justify Mr. Mueller’s continued work.

One would not know that from the president’s Twitter feed Wednesday. “This is our Joseph McCarthy Era!” Mr. Trump exclaimed, apparently not referring to his own actions. With no hint of self-awareness, the president then retweeted an image showing prominent Democrats, along with Mr. Mueller and Deputy Attorney General Rod J. Rosenstein, behind bars. “Now that Russia collusion is a proven lie, when do the trials for treason begin?” the image read.

Set aside that the president of the United States indicated his political opponents and those investigating him are traitors who should be jailed. The fact is the Russia investigation has already resulted in indictments of a range of Russian wrongdoers and exposed criminally sleazy behavior among members of Mr. Trump’s 2016 campaign. After this week, it seems Mr. Mueller is also following possible connections between people in Mr. Trump’s orbit and WikiLeaks, the website that served in 2016 as a conduit for the release of material Russian operatives stole from prominent Democrats.

Newly released emails between Jerome Corsi, a conservative conspiracy theorist, and Roger Stone, a longtime Republican trickster and Trump confidant, suggest that they communicated with WikiLeaks. Both men deny any such contact, even though Mr. Corsi told Mr. Stone, accurately, that WikiLeaks would dump a batch of stolen documents in October 2016. One question is how dishonest they may have been with investigators looking into their WikiLeaks ties. Another is whether they effectively linked Mr. Trump himself to WikiLeaks and, perhaps, Russia, a connection that the latest information does not establish.

Any reasonable prosecutor would pursue the truth in this murky picture, and the country should be glad Mr. Mueller appears to be doing so. He must be allowed to continue. Yet Matthew G. Whitaker, who has expressed hostility toward Mr. Mueller, is still the acting head of the Justice Department, three weeks after Mr. Trump fired Attorney General Jeff Sessions. It is possible for Mr. Whitaker to undermine the Russia probe in ways that would not be immediately apparent to the public. The Senate has not confirmed Mr. Whitaker for a top Justice Department post, and he is unqualified; he’s a bad choice to run the department for three weeks, three days or three hours. The Senate should be up in arms at his continuing appointment, which represents an end run around its authority to vet top executive-branch officers.

Yet GOP senators on Wednesday once again blocked a bill that would offer a measure of protection to Mr. Mueller. At the least, passing the legislation would have sent a message to Mr. Trump and Mr. Whitaker that they should keep their hands off the Russia investigation. Instead, the message the Senate sent Wednesday was one of weakness and compliance.