In any event, we did get vivid new insight yesterday into exactly how the options backdating may have occurred at Apple (AAPL), as the SEC made public its civil complaint against Heinen and CFO Fred Anderson. (For the complaint, click here.) Anderson settled the less serious charges against himself and then filed an eye-opening press release of his own.  Heinen, through her lawyer, still denies the complaint’s allegations and Anderson neither confirmed nor denied its accusations against him. (Anderson was only accused of failing to notice what Heinen was doing and failing to take affirmative steps to put things right.)

Apple, the company, is now home free, though the status of its CEO, Steve Jobs, remains slightly clouded. The SEC praised Apple for its “swift, extensive, and extraordinary cooperation,” citing in particular its “prompt self-reporting, an independent internal investigation, the sharing of the results of that investigation with the government, and the implementation of new controls designed to prevent the recurrence of fraudulent conduct.”

The cloud over Jobs stems from the written statement released by Anderson’s lawyer yesterday, which says that Anderson explained to Jobs the accounting implications of backdating in January 2001, at the time Jobs was backdating a 4.8 million-share grant to the company’s executive team, and 11 months before Jobs himself was granted 7.5 million backdated options.

The Executive Team grant, which was nominally dated January 17, 2001, worked like this, according to the SEC complaint. On January 30 Heinen emailed CEO Jobs and CFO Anderson spreadsheets laying out Apple’s stock prices for every day in the month of January, and recommending possible dates on which to retroactively date the grant. In her email to Jobs she wrote, “To avoid any perception that the Board was acting in appropriately [sic] for insiders prior to Macworld announcements, I suggest we use Jan. 10, the day after your Macworld keynote, at $16.563. That was one of the lowest closes of the month, after the $14.875 price on Jan 2. I don’t think the [Executive Team] would object to the $1.688 difference to avoid claims of inappropriate conduct.”

The email seems grimly ironic, since she evidently fears leaving the misguided appearance that they were springloading — granting options just before favorable news — when in fact they were backdating, which is even more underhanded. (How Jobs processed all this, I leave to you.)

Ultimately they settle on January 17 (stock price $17.813), and the paperwork — unanimous written consent forms, or UWCs—are drawn up falsely reflecting that board action was taken on January 17. Heinen finally collects all the signed UWCs on February 7, when the stock price is $20.75.

It’s not explained what each board member was thinking when he signed the UWCs in early February, but I suppose some may have really believed that the grant decision had been made on January 17 (though it was supposed to be the board’s decision to make, since there was no compensation committee at the time), while others didn’t examine the UWCs closely, and still others didn’t know what difference any of it would make. Still, one of the board members was Jerome York—a former CFO of IBM and Chrysler—a point former CFO Anderson emphasized in his lawyer’s statement yesterday. (York was also later named to the three-person special committee that conducted Apple’s internal investigation of the backdating. He has previously said that he recused himself from looking at decisions he was personally involved in.  The others on the committee were former vice president Al Gore, who headed it, and Google (GOOG) CEO Eric Schmidt. Schmidt was formerly CEO of Novell, which has not yet completed its own internal inquiry into backdating that occurred there during Schmidt’s tenure.)

The conversation Anderson says he had with Jobs — in which he explained the accounting ramifications of choosing any date prior to when the board had actually given its approval — would have had to occur early in the process of awarding the grant, at a time when Jobs was planning to use the Jan. 2 date for the grant (the date Heinen thought would look too much like springloading). Anderson’s attorney says that Anderson “was told by Mr. Jobs that the Board had given its prior approval and the Board would verify it.” When asked about this account by the Wall Street Journal yesterday, Jobs referred the question to an Apple spokesperson, who declined comment.

Later that year, in August, the board decided to award Jobs a huge options grant, because a previously awarded 10-million share grant was now under water. By that time, Apple had set up a compensation committee, which consisted of York, Genentech (DNA) CEO Arthur Levinson, who chaired it, and Intuit (INTU) chairman William Campbell.

On August 29 the board decided (really, really decided) to issue Jobs’s options as of that date, when the price was 17.83. But subsequently Jobs became unhappy with the vesting schedule, and he and the compensation committee began haggling over that. (Technically, matters like vesting schedules are supposed to be settled already by the time the strike date is set, so this created an awkward situation.) The haggling went on for months, with the compensation committee holding meetings on October 16 and 19, and again on November 19 and 20. (Heinen, as corporate secretary, attended these meetings.) By mid-December, the complaint says, Heinen decided that the August 29 date would “no longer withstand scrutiny,” since, among other things, Apple’s fiscal year ended in late September, the relevant information had still not been supplied to auditors at KPMG, and the SEC filing deadline for reporting an August 29 grant had passed. So on December 17 she emailed the chair of the compensation committee, Levinson, with a spreadsheet of three months worth of stock prices and some recommended dates for backdating the grant. “There are several days in October and November, following the first meeting of the Compensation Committee . . . that are close to the Aug. 29th close of $17.83,” she wrote. “I suggest using a day that the Compensation Committee held a telephone call, either jointly or individually with the members.” I assume the SEC includes that detail because it believes Heinen made that suggestion so that the company could plausibly pretend that a board decision had already been reached on one of those dates.

On December 18, when Apple’s price was $21.01, the compensation committee and Jobs finally came to agreement on the vesting schedule, and the next day Levinson emailed the full board, cc-ing Heinen, explaining that the grant date would be October 19, when the price had been $18.30. (That corresponded to the date of one of the compensation committee calls.) Levinson wrote, “For the record, I informed Nancy [Heinen] in advance of our intentions and of the above specifics to be certain we were conforming to all legal requirements/guidelines.” This assurance, presumably, was sufficient to satisfy that SEC that all the other directors did not realize that anything improper was happening. (Levinson referred a request for comment to an Apple spokesman, who referred me to the SEC’s exoneration of Apple as a company, and its glowing endorsement of Apple’s cooperation in the its inquiry.)

In January 2002, Heinen allegedly had phony board minutes drawn up to reflect a “special meeting” on October 19, and saw to it that the August 29 board minutes (which had already been approved by the full board in November) were altered, with similar changes being made to the compensation committee minutes. (None of these alterations were cleared with the board, the SEC says.) Then she allegedly signed the phony minutes and an accompanying Corporate Secretary’s certificate, affixing the latter with the corporate seal and falsely attesting that the date was then November 2, 2001.

What do people think? Everyone happy with the It’s All Heinen’s Fault theory? Honestly, I don’t know anymore.