"The fund didn't merely avoid losses, it greedily schemed to profit further by shorting Elan and Wyeth stock," said April Brooks, a senior F.B.I. official in New York, during a press conference on Nov. 20, the day Mr. Martoma was arrested.
Internal SAC trading records, according to people directly involved in the case, indicate that the hedge fund did not have a negative bet in place in advance of the announcement of the drug trial's disappointing results. Instead, the records indicated that SAC, through a series of trades, including a complex transaction known as an equity swap, had virtually no exposure — neither long nor short — heading into the disclosure of the drug data.
A different narrative surrounding the firm's trading could help Mr. Martoma, who has pleaded not guilty to securities fraud and conspiracy in what the government calls the most lucrative insider trading case ever charged.
The government, however, does have powerful evidence against Mr. Martoma. Prosecutors say the fund avoided losses by selling its roughly $700 million stake in Elan and Wyeth. If, as the government says, Mr. Martoma caused SAC to sell the shares — and then short them — while possessing important, nonpublic information, that would constitute an insider trading crime. And prosecutors have secured the testimony of the doctor who says he leaked the drug trial data to Mr. Martoma.
Still, perhaps more important, the trading records may complicate a government effort to pursue a case against Mr. Cohen. The SAC founder has not been accused of any wrongdoing, and has said he acted appropriately at all times.
In bringing charges against Mr. Martoma, prosecutors appeared to be circling nearer to Mr. Cohen. The criminal complaint against Mr. Martoma noted that Mr. Cohen had spent 20 minutes on the telephone with the portfolio manager the night before SAC began selling its shares. Prosecutors have not claimed that Mr. Cohen knew that Mr. Martoma had confidential information about the drug trials. (Mr. Martoma has refused so far to cooperate in helping the government build a case against his former boss.)
Yet if the 2008 trade is a possible avenue for the government, it is running out of time to bring a case against Mr. Cohen. Under the statute of limitations for insider trading crimes, the government would have to file a criminal case against him by mid-July. That deadline is the five-year anniversary of the trade in question, unless it could prove a conspiracy with Mr. Martoma that continued well past then.
Prosecutors have not sought to reach a "tolling agreement" with Mr. Cohen, which would allow the government additional time to bring a case past the statute of limitations, according to people briefed on the matter. The S.E.C., meanwhile, is weighing whether to file a civil fraud lawsuit against the fund connected to the drug-stock trades.
All this comes as a Feb. 14 cutoff approaches for SAC clients to ask for their money back. The fund has told employees that it expects at least $1 billion in withdrawals from the $14 billion fund amid the intensifying investigation. SAC has a standard quarterly redemption deadline.
Several other factors could make it difficult for the government to implicate Mr. Cohen. SAC is well known for its aggressive, rapid-fire trading style, and several former employees say that there is nothing unusual about the fund's exiting a large position over just a few days.
"It's one thing to bring an insider trading charge against a market novice who pours his 401(k) into a stock after hanging up the phone with an insider," said Morris J. Fodeman, a former prosecutor and now a white-collar criminal defense lawyer at Wilson Sonsini Goodrich & Rosati. "But it's far more difficult to make a case against a sophisticated hedge fund that routinely takes large positions and employs complex trading strategies."
Moreover, both inside and outside SAC, there had been much controversy and debate surrounding the effectiveness of the Alzheimer's drug, called bapineuzumab, leading up to the July 2008 release of the companies' clinical results. Mr. Martoma's colleagues in SAC's health care group raised specific concerns with Mr. Cohen about the wisdom of holding such a large position in the two companies. And while preliminary data announced by Elan and Wyeth in June offered encouraging news, they also suggested potential problems.
"We believe potentially confounding factors will continue to fuel controversy over bapineuzumab," wrote Caroline Y. Stewart, a drug stock analyst with Piper Jaffray, reacting to the preliminary results.
On July 11, another Wall Street analyst, Jonathan Aschoff at Brean Murray Carret & Company, raised red flags about a sharp run-up in the price of Elan's shares heading into the presentation of the data.
"We have numerous concerns with the clinical development of bapineuzumab, and what we viewed to be underwhelming top-line Phase 2 results make us highly doubtful of success," Mr. Aschoff wrote. "In our opinion, this strategy only serves to increase clinical risk and stoke our pessimism."
The uncertainty relating to the Alzheimer drug's clinical results could help explain what led Mr. Cohen to hedge SAC's position so that it had "neutral exposure," in Wall Street parlance, heading into disclosure of the trial results.
The short positions that SAC established in Elan and Wyeth were matched almost perfectly to offset an equity swap that effectively provided the fund with exposure to 12 million Wyeth shares, according to the SAC documents. An equity swap mimics ordinary shares and gives investors like hedge funds the benefits of stock ownership without actually owning the shares. Funds often use these complex derivatives to accumulate a large position but not tip off the market.
When government officials announced the case against Mr. Martoma, they made no mention of the swap. Instead, they emphasized how SAC had jettisoned its Elan and Wyeth shares and then brazenly accumulated short positions in both companies.
"The charges unsealed today describe cheating — coming and going," Preet Bharara, the United States attorney in Manhattan, said in opening remarks during the press conference. "Specifically, insider trading first on the long side, and then on the short side."
The government noted the swap position in its court papers, but did not factor it into SAC's overall gains and losses in Elan and Wyeth. Because SAC did not trade the Wyeth swap, instead leaving the position in place, it could not be part of any insider trading charge.
Representatives for the United States attorney's office and the S.E.C. declined to comment. An SAC spokesman declined to comment, as did Charles A. Stillman, the lawyer for Mr. Martoma.
Prosecutors have built their case against Mr. Martoma by securing the cooperation of Dr. Sidney Gilman, a neurology professor who ostensibly leaked to him the confidential data about the drug being jointly developed by Elan and Wyeth. The companies hired Dr. Gilman to oversee the clinical trials. SAC paid Dr. Gilman about $108,000 as a consultant.
The government said that Mr. Cohen's fund accumulated a roughly $700 million combined stake in Elan and Wyeth based on Mr. Martoma's recommendation. SAC's equity swap with respect to Wyeth, however, added $566 million in exposure.
On Thursday, July 17, 2008, as the drug trials neared completion, Dr. Gilman told Mr. Martoma that patients were experiencing serious side effects, the government said. Three days later, on a Sunday, with the markets closed, Mr. Martoma had the 20-minute conversation with Mr. Cohen, according to telephone records cited in the criminal complaint. Prosecutors said that Mr. Martoma told his boss that he was no longer "comfortable" with the investments.
On Monday morning, July 21, at Mr. Cohen's direction, SAC's head trader began selling the fund's 10.5 million shares of Elan and 7.1 million shares of Wyeth. By July 29 — the day that the companies announced the trial results — SAC had not only sold out of its Elan and Wyeth holdings but also established short positions in the stocks. SAC was short about 4.5 million shares of Elan and 3.3 million shares of Wyeth. The fund also purchased a small number of Elan put options, a bet that the company's shares would decline.
The 12 million-share equity swap position in Wyeth, however, counterbalanced the short exposure. SAC was short 4.5 million shares of Elan but, taking the swap into account, effectively long about 8.7 million shares of Wyeth. On July 30, the first trading day after the companies disclosed the negative trial results, Elan's stock fell about 42 percent and Wyeth's stock dropped about 12 percent.
Federal prosecutors said that SAC's trading ahead of the announcement allowed the fund to avoid $194 million in losses by exiting the Elan and Wyeth positions, and then also earn about $83 million on the short trades. But SAC also had paper losses of about $70 million on its Wyeth swap, almost entirely negating any gains from the short sales.
While such details would seem to contradict how authorities have described the trading, prosecutors could argue that SAC had little choice but to leave the swaps in place, and that was part of the strategy to trade on inside information. That is because selling a swap would be difficult to do without attracting attention in the marketplace. If SAC had sold its swaps, it would have had to notify the Wall Street bank that it entered into the swap transaction with and, in turn, the bank's trader would have most likely sold the shares on the open market.