Likewise, Bank of America was well aware of the $3.2 billion in bonuses that Merrill paid to its rank and file in late December. The two companies had agreed in September that Merrill might pay up to $5.8 billion, according to a private agreement reviewed by The New York Times.

Several weeks after that agreement was struck, a top deputy to Mr. Lewis met with Mr. Thain and asked him to lower the bonus pool below $3.5 billion and to increase the portion paid in cash. Mr. Thain agreed to do so, according to two people familiar with the meeting.

Mr. Thain, meanwhile, lobbied for a bonus of his own until December, according to people familiar with his board discussions. The initial $40 million suggestion floated on his behalf was no longer viable and Mr. Thain himself suggested a figure of $5 million to $10 million. After that number was pilloried in public, he formally asked the board to award him nothing.

On Dec. 9, Mr. Thain flew to Charlotte to attend Bank of America’s board meeting, where Merrill’s financial results through November were presented. Already 60 percent of Merrill’s losses were visible, but neither Mr. Lewis nor his board questioned Mr. Thain about the losses, according to a person close to Mr. Thain. Mr. Lewis did not immediately disclose the losses to his shareholders, who had voted to approve the merger just days before.

Mr. Lewis later said that the losses greatly accelerated in mid-December, which caught him off guard. On Friday, James Mahoney, a Bank of America spokesman said that “we have not disputed that we were kept informed about the financial condition of the company.”

During the last two weeks of December, while Mr. Thain was skiing in Vail, Mr. Lewis told federal regulators that he was thinking of backing out of the deal because of the losses. Government officials, according to Mr. Lewis, told him he had to complete the deal in order to keep markets calm. But Mr. Lewis did not tell Mr. Thain about his talks with the government until Jan. 5, according to a person close to Mr. Thain.

AS the merger closed, and a new year began, Mr. Thain was prepared to take on a leadership role at Bank of America, even though several of his top deputies, longtime Merrill leaders, began leaving the bank themselves. Mr. Lewis, battered by analyst questions about the wisdom of the Merrill takeover, became disenchanted with Mr. Thain. In mid-January, he met with Mr. Thain at Merrill’s downtown headquarters. After a five-minute meeting, Mr. Thain was out.

Furious, Mr. Thain paced the halls of Merrill, venting his frustration to at least two people. “I don’t know how these people can run this company without me,” he told them.