SEC complaints filed in federal court in California said Perry and Keys defrauded new and existing IndyMac shareholders by making false and misleading statements about IndyMac's financial condition in its 2007 annual report and in offering materials for the company's sale of $100 million in new stock to investors. In early February 2008, IndyMac said that it would return to profitability. It kept paying preferred dividends in 2008 and said it did so without having to raise new capital, according to the commission. But late that month Perry and Keys knew that IndyMac had begun raising new capital to protect IndyMac's capital and liquidity positions. The SEC said, specifically, that Perry and Keys regularly received information that IndyMac's financial condition was rapidly deteriorating, authorizing new stock sales anyway, and failing to fully disclose IndyMac's precarious financial condition in the 2007 annual report and the offering documents for the new stock sales.

According to the SEC's complaint, Abernathy replaced Keys as IndyMac's CFO in April 2008, and also made false and misleading statements in offering documents that were used to sell new IndyMac shares.

The SEC alleged, too, that in the summer of 2007, while serving as IndyMac's executive vice president in charge of specialty lending, Abernathy made false and misleading statements about the quality of the loans in six IndyMac offerings of residential mortgage-backed securities totaling $2.5 billion. He received internal reports each month revealing that 12 to 18 percent of IndyMac's loans contained misrepresentations regarding important loan and borrower characteristics. The offering documents, however, said that nothing had come to IndyMac's attention that any loan included in the offering contained a misrepresentation. The SEC, which acknowledged the FDIC's assistance in the investigation, alleged that Abernathy failed to ensure that the quality of IndyMac's loans was accurately disclosed and failed to disclose that information had come to IndyMac's attention about loans containing misrepresentations.