On Monday, Tribune Company, the jobs-shedding media conglomerate, filed for bankruptcy, casting a heavy cloud over its future.

But then came Tuesday, and the two count federal criminal complaint against Illinois Governor Rod Blagojevich, which describes an attempt by the governor and his chief of staff, John Harris, to leverage at least $100 million in state funds for the Chicago Cubs—owned by Tribune Company since 1981—in exchange for changes to the paper’s editorial page, possibly including firing the entire board.

What was Tribune’s response to this corrupt bargain? We don’t know. But, according to Harris’ reports to his boss, it wasn’t a plain, firm, “No.”

That, along side the rest of the complaint, raises a lot of uncomfortable questions to which Zell presumably knows the answers. Until we hear from him, the implications aren’t pretty.

The governor’s scheme looks like it was hatched during a series of taped phone calls in early November. The indictment describes how Blagojevich suggested that an advisor compile a package of the Chicago Tribune’s negative coverage of his administration, and pointedly raise it in a discussion of the Cubs assistance. But even that veneer of subtlety gives way in subsequent conversations. “Our recommendation,” the governor says in one, “is fire all those fucking people, get ‘em the fuck out of there and get us some editorial support.”

Blagojevich has been in hot water from the earliest days of his administration, and that’s led him to come under frequent criticism from the Tribune’s editorial page. Twice this fall, the editorial board asked state legislators to investigate grounds for impeachment. But it seems that a Tribune editorial from November 3, knocking the way the governor distributed state funds without legislative or voter approval, particularly raised Blagojevich’s ire. The governor hoped to use a contradiction he saw between that editorial criticism and the parent company’s request that Blagojevich take title of the Cubs’ Wrigley Field, which would save the Tribune upwards of $100 million. In two conversations, Blagojevich makes it clear that he was especially upset with John McCormick, a deputy editorial page editor, and wanted to see him fired.

On November 5, gubernatorial chief of staff John Harris made the governor’s case to someone the complaint identifies only as “Tribune Financial Advisor.” Harris says the advisor told him it was a delicate request, but agreed to sound out “Tribune Owner”—Zell. Harris also says the advisor asked to meet Harris in person to discuss the request.

In a later call, Harris says he met the Tribune advisor the next Monday. Recounting their conversation, Harris told the governor that the advisor assured him that Tribune Owner “got the message and is very sensitive to the message.” Harris also said he was told that “certain corporate reorganizations and budget cuts [were] coming and, reading between the lines, he’s going after that section”—i.e. that he believed that Zell had the Trib’s editorial board in his crosshairs. The governor asked Harris if Tribune understood that the Cubs deal was in jeopardy if changes weren’t made soon, and Harris said they did.

In a taped call from November 21, Blagojevich pressed Harris on his progress, remarking that “the Tribune thing is important, if we can get that.” Harris told his boss that the request was “delicate, very delicate,” but promised to press ahead.

When the Tribune announced eleven staff cuts on December 4, Blagojevich’s press secretary called the governor to say that McCormick was not among them. The next morning, Harris and the governor spoke again, and Blagojevich asked if “there’s still more coming.” Harris assured him that “they’ve got a lot of cuts to make,” and the two resolved to contact the Tribune advisor again.

Where does that leave Tribune? United States Attorney Patrick Fitzgerald said he was “not going to opine” on how the Tribune Company responded to governor’s offer. And Tribune, in a statement, denied any wrongdoing:

[T]he actions of the company, its executives and advisors working on the disposition of Wrigley Field have been appropriate at all times. No one working for the company or on its behalf has ever attempted to influence staffing decisions at the Chicago Tribune or any aspect of the newspaper’s editorial coverage as a result of conversations with officials in the governor’s administration.

That’s followed by a quote from Chicago Tribune editor Gerould Kern denying that Tribune corporate has ever contacted him to complain about the paper’s editorials, or to influence its coverage of the governor.

But the statement leaves a few questions unaddressed.

*Did the financial advisor make the deal that Harris implied he did?

*Did Zell “get the message” from the advisor, as Harris says he was told he did, and, if so, what did he do about it?

*Did Zell or anyone else at Tribune corporate contact law enforcement about the governor’s offer? Did they contact anyone at the Tribune’s newsroom?

*Fitzgerald says the Tribune had been prepared to run a story on the wiretaps eight weeks before the investigation went public, but agreed to hold the story. Was Zell involved in or did he know about the Tribune’s decision not to publish?

*Did the Tribune know the investigation was coming into its backyard, and if so, was that information passed on to executives at the Tribune Company before Fitzgerald made it public? If so, when?

*And who’s that Tribune Financial Advisor, and what does he have to say?

With so many questions striking at Sam Zell and Tribune’s ethical conduct, we need a full accounting to assure readers and other Tribune stakeholders that he remains fit to lead a respectable newsgathering organization, one that is unwilling to compromise the most basic principles of journalistic independence, even in the face of dire financial circumstances.

Time’s wasting.