FORTUNE — Ever since the Raj Rajaratnam trial began, many have wondered why the government is cracking down on insider trading when the public thinks that there are bigger crooks to nail — namely the executives and employees who worked at the firms involved in the great financial meltdown of 2008.

While insider trading is certainly a crime, it seemed like a bit player in the drama that began when the housing bubble burst. Banks and insurance companies involved in the credit crisis seemingly wrought greater devastation on the economy and investors than a crew of greedy money managers, critics contend. For example, Rajaratnam allegedly made $54 million in profits and avoided about $9 million in losses. By comparison, AIG lost $99 billion in 2009, needed an astronomical bailout, and helped usher in a recession so severe that it drove unemployment to double-digit levels.

But Preet Bharara, the US Attorney for the Southern District of New York, just answered those critics. His office sued Deutsche Bank (DB) today, seeking triple damages and penalties under the False Claims Act.

The government accused the bank and its subsidiary MortgageIT of lying about the quality of some mortgages that were to be insured by the government. With the government insurance, Deutsche Bank and MortgageIT were allegedly able to sell weak mortgages for more than they were worth. Because the mortgages were weak, the FHA has been forced to honor insurance policies on the loans.

“You can always get someone up on charges if you work hard enough given all the regulations we have,” says Ed Novak, an attorney at Polsinelli Shughart. “I don’t buy that the financial industry has so weakened the statutory framework of this country that we can’t pursue something.”

The details of the allegation may be special to Deutsche Bank, but the story has the same general characteristics of so many schemes unearthed in the aftermath of the financial meltdown. A bank takes weak mortgages and finds a way to sell them for more money to unsuspecting investors, passing the risk onto others while making a profit.

It is easy to forget that the system moves more slowly that we’d like. Even in the case of Enron, it took years for justice to be served. The indictments moved at a quick pace due to the company’s high profile collapse (and having a whistleblower didn’t hurt), but the process still took years. Cracks were visible at Enron in 2001, the year it filed for bankruptcy. Congress held an inquiry in 2002, and smaller players were indicted. But it not until 2004 were former CEO Jeff Skilling and ex-chairman and CEO Ken Lay indicted. The trials dragged on through the spring of 2006.

While Bharara was being panned for ignoring financial crisis-related fraud, it seems his office was working on the Deutsche Bank case all along. “It takes time to fight against people with great lawyers and lots of money, who did many things behind a wall of fine print designed to absolve them of responsibility for reckless behavior,” says Novak.

When it comes to the question of whether the government will go after the bad guys of the financial crisis, the jury is still out. But it’s clear that there’s more going on at the office of the US Attorney for the Southern District than meets the eye.

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In Rajaratnam news…

Rajaratnam’s lead defense attorney, John Dowd, kept up a good gravel-voiced, tough-talking grandpa act throughout the trial. The 69-year-old Akin Gump partner lived up to the “lovable curmudgeon” billing that Reuters gave him when the proceedings began, coolly dismissing the government and its witnesses. (The prosecution’s case was “make believe.” Anil Kumar’s testimony is a “monstrous lie.” Danielle Chiesi was spouting “self promotional gibberish.”)

But the lawyer who famously defended John McCain and Pete Rose can lose his cool. He told reporters Monday: “I hate you, I’m not telling you a thing;” and he maybe flipped off a camera guy.

And Dowd has hurled more than insults in the past.

“John Dowd indeed took a swing at me on a street in front of the Federal Courthouse during the 1997 [Fife] Symington trial,” says John Dougherty, a long time investigative journalist who covered the Symington case, as well as the Keating Five. (He also made an unsuccessful run for US Senate.)

After asking a barrage of questions, Dougherty says that Dowd called him “a real asshole,” to which Dougherty replied that the feeling was mutual. Dowd responded by throwing a punch (breaking only a tape recorder), and the incident was later noted in the Arizona Republic.

If the jury comes back with a guilty verdict, beware.

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Notes from behind the hedge…

** Och-Ziff is up about 4% and inflows have pushed assets under management to $29.4 billion. But the company reported a first quarter earnings loss.

** Man Group raised $1.5 billion for a Japan fund.

** Hedge funds, Swiss private banks, and an Abu Dhabi investment vehicle will back the Glencore IPO.

** A Nashville pension fund will invest $85 million in hedge fund run by Marvin Bush, brother of GW Bush.

** Small hedge funds finally getting some love from institutional investors.

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