(FORTUNE Magazine) – The mole has turned.

Mark Whitacre, the FBI informant whose covert tape recordings forced Archer Daniels Midland to plead guilty to the costliest criminal price-fixing conspiracy in U.S. history, is blowing his whistle again. This time, though, his target isn't his erstwhile employer, which has already agreed to pay a record-breaking $100 million in fines for rigging prices in two agricultural commodities. Now Whitacre is fingering the FBI itself, accusing one of its agents of ordering him to destroy evidence, denying him access to lawyers and doctors, and driving him to the brink of suicide. And once again, he says his charges are backed up by tapes.

Whitacre's allegations--outlined in a lawsuit scheduled to be filed on Monday, January 13, and detailed in an exclusive interview with FORTUNE (see following article)--are the latest salvo in the extraordinary war that has broken out between the government and its onetime informant. In December, in a stunning development, a federal grand jury indicted Whitacre for price fixing, charging him, along with two of his former ADM colleagues, with some of the very crimes he exposed.

If Whitacre's complaints against the FBI hold up, the government's case against the ADM executives could be destroyed. Whitacre's charges also could scuttle the Justice Department's ongoing investigation into price fixing in the agricultural processing industry. But what's crucial to such a scenario is the answer to this question: Is the 39-year-old Whitacre, a man who has for so long lived a life of deception, actually telling the truth?

To buttress his accusations, Whitacre, who is now chief executive of a North Carolina biotechnology company, says he has witnesses and documents. He has also made tapes. Whitacre, who taped his colleagues at ADM for 22 years, now reveals that he was also spying on his spymasters at the FBI and the Justice Department from 1993 to 1996. Whitacre says those tapes are no longer in his possession, but sources say that the originals, as well as several sets of copies, still exist.

The government is desperately trying to get its hands on any tapes Whitacre may have made. In late December, FORTUNE has learned, the public integrity section of the Justice Department's criminal division launched an inquiry into allegations that the FBI instructed Whitacre to destroy or withhold evidence. In early January, Justice wrote to Whitacre's lawyers requesting any "tapes and transcripts corroborating these charges of official misconduct."

Will Justice get those cassettes? That's unclear. "The government wants the original material," says Bill Walker, one of Whitacre's lawyers. "That would be like giving the fox the right to count the eggs in the hen house. My concern is, what proof do we have that the material existed if it somehow disappears after they get it?"

The following are Whitacre's allegations against the government and ADM officials, from statements in both the lawsuit and his interview with FORTUNE:

--On at least four occasions, charges Whitacre, an FBI agent told him to destroy price-fixing tapes that the agent considered to be unfavorable to the case.

--Whitacre claims federal agents violated his constitutional rights by denying him timely access to a lawyer and doctor, even after he discussed the possibility of killing himself in 1993.

--Whitacre, for the first time, discloses that he is under treatment for bipolar disorder, a psychiatric condition most commonly known as manic-depressive illness. It was abuse by the FBI, he charges, that triggered the onset of his disorder in 1993--and led him to attempt suicide in the summer of 1995.

--At no time, Whitacre contends, did the FBI read him his Miranda rights, which would have warned him that he himself was a suspect in the price-fixing investigation.

--Whitacre accuses the Justice Department of ignoring tape-recorded evidence that showed Dwayne Andreas, ADM's politically connected chairman, being briefed on price-fixing negotiations.

Brian Shepard, an agent in the FBI's Decatur, Illinois, office, is expected to be named in Whitacre's lawsuit and is the target of most of his accusations. He has specifically declined to comment on the allegations. So have an FBI spokesperson and Scott Lassar, First Assistant U.S. Attorney in Chicago and the co-lead counsel in the central price-fixing investigation. James Epstein, Whitacre's former lawyer, couldn't be reached by press time. Neither could Dwayne Andreas.

Those who have followed this case know that it has more twists and turns than a Raymond Chandler mystery. Mark Whitacre, once the president of ADM's fast-growing BioProducts division, was widely considered a leading candidate to become the company's next president. His division's flagship product was lysine, an animal feed additive derived from corn. In 1992, Whitacre's lysine plant was having production problems. Suspecting that the plant was being sabotaged by a Japanese competitor, Dwayne Andreas called on a friend at the CIA--yes, the CIA--to investigate. Eventually the CIA turned the case over to the FBI.

As part of its investigation, the FBI wanted to record Whitacre's home phone conversations with someone in Tokyo whom ADM suspected of being involved in the alleged sabotage. That put Whitacre in a bind because he was also involved, allegedly at the behest of his bosses, in preliminary price-fixing discussions with the Japanese, using another phone line. What was to stop the feds from listening in on that line as well, Whitacre wondered?

So when special agent Brian Shepard showed up in November 1992 to install a recorder at Whitacre's home, the executive--prodded by his wife, Ginger--decided to tell the truth about the aborning price-fixing scheme. Within weeks Whitacre was secretly taping his colleagues, and by January he had signed a cooperation agreement officially designating him an undercover informant.

The information Whitacre gathered in his 2 1/2 years as a mole was potent enough to induce ADM to plead guilty last October to conspiring to fix the prices of lysine and citric acid, commonly used for food flavoring. Then, in December, a federal grand jury indicted executive vice president Michael Andreas (Dwayne's son and onetime heir apparent) and Terrance Wilson, former head of ADM's corn-processing division. The same panel also indicted Mark Whitacre. All three men have pleaded not guilty.

Why did the Justice Department turn so forcefully on its own informant? Actually, there has been bad blood between the parties for quite some time--ever since August 1995, when Whitacre admitted he had garnered millions of dollars in off-the-books payments from ADM. The company says he embezzled the money; he says it was part of an offshore compensation scheme approved by top management. Prosecutors contend the payments violated Whitacre's immunity agreement with the Justice Department.

But even if Whitacre did steal money, why did the government indict him for price fixing? The informant says the charge was supposed to be part of a deal worked out between U.S. Attorney Lassar and Whitacre's former lawyer Epstein. Whitacre would have pleaded guilty to some sort of fraud charge (to date, he has not been indicted for fraud) in Springfield, Illinois, and to a price-fixing charge in Chicago. Justice would have then moved to consolidate the two cases in the courtroom of a judge in Chicago, one who would supposedly have then been disposed to treat him leniently at sentencing. Whitacre, unwilling to plead guilty to a crime he says he didn't commit, not only rejected the deal but also fired Epstein.

Justice has also suspected Whitacre of hoarding tapes. In November a grand jury issued a subpoena demanding that he turn over all tapes made for the FBI and of the FBI. Whitacre was summoned to appear before a grand jury in Chicago on November 18. The panel asked him four questions about tapes. He took the Fifth Amendment on each one.

In the following interview, Whitacre will lay out his version of events, which is damning to FBI agents, his former lawyers, and prosecutors. But can someone who simultaneously led three separate lives--hotshot executive, mole for the FBI, and mole against the FBI--actually present one indivisible version of reality? Can a person under treatment for bipolar disorder, which in its most manic manifestations can cause patients to experience delusions, adequately distinguish between fact and fantasy? (Whitacre says he has been able to control his condition by taking lithium.)

FORTUNE first interviewed Mark Whitacre in the summer of 1995, about one month after his role as a mole had been prematurely exposed. His account of the price-fixing scheme, including details of specific meetings between ADM and Japanese competitors, turned out to be strikingly similar to the crimes ADM admitted to when it pleaded guilty more than a year later, in October 1996. He was right on that score.

But there are reasons to be skeptical. Back in 1995, he had not one ill word to say about the FBI. In fact, he praised Brian Shepard, the agent he now charges with causing him unbearable stress, as "a very trustworthy guy," adding that "we really hit it off well." As recently as last fall, a journalist from WAND-TV in Decatur asked Whitacre if his trust in Shepard had ever been betrayed. His reply: "No, not at all. Not at all."

So why is Whitacre only now telling his story about the FBI--four long years after he started working as a mole? Actually, he wanted to raise the issue 18 months ago. In July 1995, Whitacre sent a fax to James Epstein, his lawyer, saying, "I still see more wrong doing [sic] by the FBI, then [sic] by ADM. I think that you should tell the Justice Dept. this stuff..." Whitacre says Epstein advised him to hold his fire--that he already had one very powerful enemy in ADM and that he didn't need to take on the FBI and the Justice Department as well.

Next chapter in the Mark Whitacre story? His new lawyers expect the government to hit back hard. Says Bill Walker, one of his attorneys: "I fear that Mark is in for further retaliation in the very near future for doing this." The possibilities, says a Justice Department source, include indictments for fraud and obstruction of justice.

Meanwhile, lawyers for Whitacre's co-defendants have latched on to the idea that something went terribly awry in the FBI's investigation. "We are going to allege, and we are going to attempt to prove, and we believe we can prove, that this case is the mother of all out-of-control undercover operations," Terrance Wilson's lawyer, Reid Weingarten, told a federal judge in Chicago in December. Ironically, the man who exposed one of corporate America's great scandals may now deliver the information that helps Mick Andreas and Terry Wilson--his archenemies--beat the rap.