Is it time to start wondering about the future of Wall Street’s independent investment banks? It’s almost unthinkable, but news broke Sunday evening that Merrill Lynch & Co. (MER) had agreed to sell itself to Bank of America Corp. (BAC) as the U.S. financial markets went through one of the most tumultuous weekends in history. The Wall Street Journal reported Sunday that Merrill had agreed to a deal worth an estimated $44 billion, roughly $29 per share, with the boards of both companies approving the deal on Sunday. Shares had closed at $17.05 on Friday, bitten by concerns over Lehman Brothers Holdings Corp. (LEH); Lehman itself is expected to file for bankruptcy before market open on Monday morning, after Feds made it clear they wouldn’t step in and other potential buyers of the troubled investment bank backed away. It’s a deal that will literally reshape American banking, and puts BofA in a position few might have imagined to start the year; the North Carolina bank purchased troubled mortgage lender Countrywide Financial Corp. on July 1, making it the largest lender and servicer in the country. The addition of Merrill will give it the nation’s largest stock brokerage and a large investment bank to boot. Neither company had commented on the reported deal by the time this story was published. “Why would Bank of America do this?” analyst Nancy Bush at NAB Research LLC told the Journal. “Ken Lewis always likes to buy the biggest thing he can. So why not this? You are master of the universe, basically.” Key sources told HW that talks between BofA and Merrill gained steam after the New York Fed convened a top-level meeting this weekend to discuss the future of Lehman; BofA had been rumored to be involved in bidding for the company, according to earlier reports. One source, close to BofA, told HW Sunday night on condition of anonymity that the discussions involving Merrill had begun because BofA saw more value in the franchise and Merrill CEO John Thain knew that Lehman’s failure put his firm “next in line for the Bear Stearns mantle.” Thain took the helm at Merrill last October after former CEO Stan O’Neil was ousted amid a burgeoning credit crisis and the firm’s mortgage exposure; the firm has since raised billions of dollars in fresh capital and has sold off key troubled assets. Which means that beyond Lehman, we now have to consider the potential fate of both Morgan Stanley (MS) and even Goldman Sachs (GS). “The fate of both Morgan Stanley and Goldman Sachs will be front and center Monday morning, as the Street wakes up to a world where the independent broker-dealer are increasingly thin in number,” according to the Journal’s report. “This tumultuous year has made it clear that investment banks like Lehman and Bear Stearns face vulnerabilities that commercial banks such as J.P. Morgan and Bank of America are less prone to.” Dow Jones futures were trading off 311 points when this story was published — we hope all of our readers are strapped in for what promises to be an incredibly wild day on Monday. Disclosure: The author held no relevant positions when this story was published; indirect holdings may exist via mutual fund investments. HW reporters and writers follow a strict disclosure policy, the first in the mortgage trade.