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When Tony West arrived in a Justice Department conference room to put the finishing touches on a lawsuit against JPMorgan Chase, he saw a familiar number flash on his cellphone.

Jamie Dimon, JPMorgan’s chief executive, was calling to seek a rare face-to-face meeting with Mr. West, a top Justice Department official with close ties to President Obama. Mr. Dimon hoped the meeting would avert the lawsuit, which threatened to spotlight the bank’s questionable mortgage practices before the financial crisis.

Mr. West, 48, a soft-spoken but imposing presence, resisted the overture. Pacing around the room with the phone pressed against his ear, people at the meeting later recalled, he told Mr. Dimon that the Justice Department would meet only if the bank came with a more generous offer than the $3 billion it had proposed to settle a narrow window of cases.

“We don’t want you to waste your time and we don’t want to waste the attorney general’s time,” he told the bank chief, according to people in the room.

Mr. Dimon agreed to raise his offer, prompting the government to postpone the lawsuit. Two days later, on Sept. 24, he arrived at the Justice Department in Washington, where the two sides worked toward a $13 billion settlement that was announced on Tuesday.

The settlement amounts to roughly half the bank’s annual profit.

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Mr. West’s negotiating tactics underscore a broader strategy shift at the Justice Department, where prosecutors are seeking to hit Wall Street where it hurts most: the bottom line. After critics faulted the Justice Department for imposing fines considered little more than a slap on the wrist, Mr. West and Attorney General Eric H. Holder Jr. have signaled to the nation’s biggest banks that the billion-dollar mark is now a floor rather than a ceiling.

The deal with JPMorgan, which eclipses other Wall Street settlements, is the largest sum a single company has ever paid to the government. The bank, at the Justice Department’s insistence, also admitted to a statement of facts that outlined how it failed to fully disclose the risks of buying risky mortgage securities from 2005 to 2008.

And the case, a symbol of the government’s wider crackdown on Wall Street’s sale of troubled mortgage securities to pension funds and other investors, may set a precedent for cases against other major banks and industries like health care, where fines have already swelled in recent years.

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“The size and scope of this resolution should send a clear signal that the Justice Department’s financial fraud investigations are far from over,” Mr. Holder said in a statement. “No firm, no matter how profitable, is above the law, and the passage of time is no shield from accountability.”

In its own statement, JPMorgan noted that it had money set aside for the settlement. And Mr. Dimon added, “We are pleased to have concluded this extensive agreement.”

Mr. West, who twice sought political office in his native California and is a former defense lawyer who once represented John Walker Lindh, the American who joined the Taliban in Afghanistan, declined to be interviewed for this article.

But people who have worked alongside Mr. West say steep fines are central to his negotiating philosophy, reflecting a focus on deterring repeat behavior. Even multimillion-dollar penalties, he has told colleagues, might become only the “cost of doing business” for big banks.

Still, some critics of Wall Street are seeking harsher penalties. They question why the Justice Department’s has pursued civil penalties, rather than criminal charges, against the nation’s biggest banks.

“Unless you hold the executives accountable, it really is just the cost of doing business,” said Bart Naylor, a policy advocate at Public Citizen, who noted that the settlements hurt shareholders more than executives.

And during a conference call on Tuesday, Marianne Lake, JPMorgan’s chief financial officer, emphasized that $7 billion of the settlement was tax-deductible. A person briefed on the case said the decision whether to credit the payments ultimately rested with the I.R.S., though public interest groups remained concerned.

In contrast, lawyers for big banks have questioned whether the Justice Department is crossing a line. The fines, they complain, are arbitrary figures meant as a kind of catharsis for the public.

Mr. West’s pursuit of big fines came into focus during the civil prosecution of Standard & Poor’s, which the Justice Department accused of awarding top ratings to troubled mortgage investments. While the rating agency offered a roughly $100 million settlement, the Justice Department sought a penalty of more than $1 billion and an admission of wrongdoing, people briefed on the matter said. The Justice Department ultimately filed the lawsuit and continues to press its case.

The breakdown of the $13 billion settlement with JPMorgan includes a $2 billion fine to prosecutors in Sacramento and $4 billion in relief to struggling homeowners in hard-hit areas like Detroit and certain neighborhoods in New York. The government earmarked the other $7 billion as compensation to federal agencies and state attorneys general across the country, including those in Illinois, New York and California. The California attorney general, Kamala Harris, is Mr. West’s sister-in-law.

The Justice Department secured a range of other concessions, including admitting to the statement of facts. JPMorgan also backed down from demands that prosecutors drop a related criminal investigation into the bank, and it forfeited the right to try later to recoup any of the $13 billion from the Federal Deposit Insurance Corporation.

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Although the case thrust Mr. West into the public spotlight, his influence behind the scenes has been felt for years. Mr. West, who was president of the Stanford Law Review, joined the Justice Department under President Bill Clinton. He then returned to California as a federal prosecutor and official at the state attorney general’s office, before mounting unsuccessful campaigns for the city council in San Jose, his hometown, and the California state assembly.

Mr. West remained in politics, becoming then-Senator Barack Obama’s finance co-chairman in California. On the morning Mr. Obama announced his candidacy for president in Springfield, Ill., Mr. West worked out with him in the hotel gym.

When Mr. Obama won the presidency, he nominated Mr. West as head of the civil division at the Justice Department. In that role, Mr. West oversaw financial crisis cases against companies like S.&P., led the Justice Department’s lawsuit against Arizona’s immigration law and played a role in the decision not to support the Defense of Marriage Act in a Supreme Court challenge.

“He almost single-handedly raised the profile and influence of the civil division to historic levels,” said Ted Wells, a prominent trial lawyer and partner at Paul Weiss, who has represented several clients before Mr. West.

Despite the contentious negotiations with JPMorgan, colleagues say, Mr. West refrained from the sort of table-pounding tactics many litigators employ. Lisa Madigan, the Illinois attorney general, has called him “unfailingly pleasant.”

Mr. West, Mr. Holder said in an interview, “will kill you not with kindness but with facts.”