A federal judge hearing arguments Wednesday in a lawsuit related to the halted John Doe probe into Gov. Scott Walker’s campaign poked at the Wisconsin Supreme Court’s rationale for ending the investigation.

Former Walker aide Cindy Archer filed the lawsuit last summer claiming Milwaukee County District Attorney John Chisholm violated her constitutional rights when his investigators executed a search warrant at her home in September 2011 as part of a John Doe investigation into Walker’s Milwaukee County office.

Chisholm also took a lead role in a second John Doe investigation into suspected coordination between Walker’s campaign and the Wisconsin Club for Growth. The Wisconsin Supreme Court ended the investigation last summer saying it was based on an invalid legal theory and ordered all evidence collected in the investigation be turned over to it. Chisholm may appeal the decision to the U.S. Supreme Court.

On Wednesday, U.S. District Judge Lynn Adelman heard arguments on whether to dismiss the Archer lawsuit, and also whether he should allow Chisholm to hold on to the evidence while the lawsuit plays out, potentially overriding the Wisconsin Supreme Court’s directive for him to return it.

The hearing was also a rare opportunity for the public to hear lawyers argue in open court on both sides of what has become a contentious legal battle with broad political implications. The Wisconsin Supreme Court, which decided not to hear oral arguments before making its 4-2 decision last summer, invalidated long-standing Wisconsin rules that campaigns aren’t allowed to coordinate with supposedly independent groups that sponsor thinly veiled political ads.

In grilling Archer’s lawyers, Adelman, a former Democratic state lawmaker appointed to the federal bench by President Bill Clinton, noted no court had previously held that such unregulated coordination is protected by the First Amendment.

“Is that a new federalist court we have now?” Adelman asked, suggesting the state Supreme Court is interpreting the First Amendment more broadly than the U.S. Supreme Court.

Adelman also argued with lawyers on both sides about how to preserve evidence in the John Doe probes for the purposes of the lawsuit.

Archer contends the two John Doe investigations were part of a pattern of retaliation against Walker and his associates because of their political views. Chisholm emphasized the first John Doe, which netted six convictions of Walker aides and associates for various crimes, was authorized by an impartial judge.

Both sides agreed that Chisholm can retain evidence collected in the first John Doe probe but disagreed about what to do with evidence from the second John Doe.

Chisholm’s lawyers raised the concern that if evidence is turned over to the Supreme Court it could be destroyed, a possibility Archer’s lawyer said was laughable.

Adelman, expressing concern about simultaneously contravening the Wisconsin Supreme Court’s order and obstructing Chisholm’s ability to defend himself, suggested that the U.S. district court clerk retain a copy of the records under seal until the lawsuit is resolved.

David Rivkin, representing Archer, said Chisholm doesn’t have the legal authority to retain access to evidence that was seized in an invalidated John Doe proceeding. But Adelman interrupted him, saying, “You’re just not addressing my issue” of how to allow Chisholm access to the records for the lawsuit while also complying with the state Supreme Court order.

Samuel Leib, a lawyer representing Chisholm’s investigators, interjected at one point saying, “This is about creating a fog.”

“They will never agree with the court in an effort to make this fair,” Leib said. “They don’t want to be fair about this. They want to pursue a political agenda.”

Rivkin called the hearing “less than the collegial debate I’m used to.”

Rivkin also represents Wisconsin Club for Growth director Eric O’Keefe, who attended the hearing but declined to comment.

O’Keefe, a conservative political activist, was one of the named targets of the John Doe investigation who filed a federal lawsuit seeking to stop that probe. U.S. District Judge Rudolph Randa, who was appointed by President George H.W. Bush, issued an order halting the probe, but he was overruled by the U.S. 7th Circuit Court of Appeals, which said the case was a matter for the Wisconsin Supreme Court to decide.

The second John Doe investigation focused on Walker’s role in coordinating with the Wisconsin Club for Growth as a vehicle for raising millions of dollars from undisclosed donors and distributing money to issue-advocacy groups for thinly veiled political ads that ran during the 2011 and 2012 recall elections.

Walker was never charged in either investigation, though the head of the state Government Accountability Board’s ethics division said he was always the primary target.

Capital W: Plug in to Wisconsin politics

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