Mueller
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The Order appointing Mueller concerns election interference, not post-election political decisions of the winning candidate.

Michael Flynn pleaded guilty last week to lying to FBI investigators regarding conversations Flynn had with the Russian Ambassador in late December 2016, barely three weeks before the Trump administration was sworn into office.

Such transitions contact with foreigners are routine, and took place during prior administrations, including the Obama administration. That makes perfect sense, since an incoming administration needs to hit the ground running with its foreign policy. Certainly there would have been howls of outrage from the media and Democrats had the incoming Trump administration waited until after the inauguration to make contact with our primary geo-political foes; it would have been portrayed as a sign of incompetence and amateurishness.

There was nothing illegal about Flynn speaking with the Russian ambassador and others. But he ran afoul of the law when he lied about it to the FBI.

It is clear from the prosecution of Flynn that Mueller views the transition as within the scope of Mueller's investigation, otherwise there would have been no reason for Mueller to prosecute Flynn. The lying took place before Mueller was appointed and did not concern conversations during the Trump campaign. For lying to the FBI when he did, Flynn could have been prosecuted by DOJ itself.

Yet Mueller's team took it on themselves to prosecute the case involving a crime (lying) that took place after the new administration was sworn in regarding a conversation during the transition. The public documents regarding Flynn's plea make clear that the transition is in focus.

If news reports have any credibility (and they may not), then Mueller is investigating the political actions of the Trump transition team during the transition period.

What authority, however, gives Mueller power to investigate the political strategies of the incoming Trump administration long after the election was over? It does not appear that Mueller has that power under the Order appointing him as Special Counsel.

In Order No. 3915-2017, Mueller was appointed with a specific mandate, to continue an investigation started by James Comey into Russian interference in the election:
(a) Robert S. Mueller III is appointed t() serve as Specia] Counsel for the United States Department of Justice.
(b) The Special Counsel is authorized to conduct the investigation confirmed by then-FBI Director James 8. Corney in testimony before the House Permanent Select Committee on Intelligence on March 20, 2017, including:
(i) any links and/or coordination between the Russian government and individuals associated with the campaign of President Donald Trump; and
(ii) any matters that arose or may arise directly from the investigation; and
(iii) any other matters within the scope of 28 C.F.R. § 600.4(a).
(c) If the Special Counsel believes it is necessary and appropriate, the Special Counsel is authorized to prosecute federal crimes arising from the investigation of these matters.
At the March 20, 2017 hearing, Comey described the investigation as relating to election interference:
As you know, our practice is not to confirm the existence of ongoing investigations, especially those investigations that involve classified matters, but in unusual circumstances where it is in the public interest, it may be appropriate to do so as Justice Department policies recognize. This is one of those circumstances.

I have been authorized by the Department of Justice to confirm that the FBI, as part of our counterintelligence mission, is investigating the Russian government's efforts to interfere in the 2016 presidential election and that includes investigating the ature of any links between individuals associated with the Trump campaign and the Russian government and whether there was any coordination between the campaign and Russia's efforts. As with any counterintelligence investigation, this will also include an assessment of whether any crimes were committed.
(Full transcript here)

Comey's reference to a "counterintelligence investigation" clearly was in the context of the preceding sentence of interference in the election. So to the extent the Order governs Mueller's authority, that authority is limited to the election-related matters, including counterintelligence investigations related to the election.

Mueller cannot successfully argue that the political discussions during the transition fall under his power, under the Order, to investigate under 28 C.F.R. § 600.4(a), which concerns "federal crimes committed in the course of, and with intent to interfere with, the Special Counsel's investigation, such as perjury, obstruction of justice, destruction of evidence, and intimidation of witnesses." There was no Special Counsel investigation during the transition, so there was nothing with which the Trump transition team could interfere.

Deputy Attorney General Rod Rosenstein takes the position that Mueller can prosecute any crimes he finds:
Rosenstein said special counsel Robert S. Mueller III can investigate any crimes that he might discover within the scope of his probe, but the deputy attorney general would not discuss which individuals are the subject of their inquiry. The interview comes days after Trump said he believes it would be inappropriate for Mueller to dig into Trump family finances.

"The special counsel is subject to the rules and regulations of the Department of Justice, and we don't engage in fishing expeditions," Rosenstein said when asked about the probe in an interview on "Fox News Sunday."
Could Mueller start investigating street crimes, acting as a roving District Attorney across the land? Just because he found a crime, could he prosecute it, even if not within the proper scope of his investigation?

Rosenstein acknowledged the limits of Mueller's powers:
"If he finds evidence of a crime that is within the scope of what Director Mueller and I have agreed is the appropriate scope of this investigation, then he can," Rosenstein said. "If it's something outside that scope he needs to come to the acting attorney general, at this time me, for permission to expand his investigation."
Has Rosenstein given Mueller the authority to investigate the political strategies of the incoming administration during the transition? If so, that would be news.

The danger the Mueller investigation's apparent overreach poses goes beyond the potential harm to individuals under investigation or prosecution.

To the extent Mueller's team is investigating the political decisions and strategies of the incoming Trump administration during the transition period, it amounts to an interference in the post-election political process and is beyond Mueller's authority.