DEERFIELD, Ill. — Walgreens Boots Alliance Inc. (WBA) announced that it is scrapping its plans to buy Rite Aid Corp. and instead will acquire only a portion of the drug store chain, after the original takeover effort seemed doomed by the Federal Trade Commission.

The new agreement replaces a previous merger deal with Rite Aid and a proposed divestiture transaction with Fred’s Inc.

The companies announced that they would end their original deal in which WBA would have purchased Rite Aid for as much as $7.37 billion. Under the new agreement, WBA will pay $5.18 billion to buy 2,186 stores, leaving Rite Aid as a regional chain. The 2,186 stores that are included in the agreement are primarily located in the Northeast, Mid-Atlantic and Southeastern regions of the United States. The three distribution centers that are also included in the agreement are located in Dayville, Conn.; Philadelphia; and Spartanburg, S.C.

The consideration for the transaction will be $5.18 billion in cash, the assumption by WBA of the related real estate leases and the grant of an option to Rite Aid — exercisable through May 2019 and subject to certain conditions — to become a member of WBA’s group purchasing organization, Walgreens Boots Alliance Development GmbH. WBA will also assume certain limited store-related liabilities as part of the new transaction.

“This new transaction extends our growth strategy and offers additional operational and financial benefits,” remarked WBA executive vice chairman and chief executive officer Stefano ­Pessina. “This deal will also allow us to expand and optimize our retail pharmacy network in key markets in the U.S., including the Northeast, and provide customers and patients with greater access to convenient, affordable care.

“We believe this new transaction addresses many competitive concerns previously raised with respect to the prior transaction and will streamline and simplify the transition for customers, team members and other ­stakeholders.”

The new agreement replaces the previous merger deal with Rite Aid, announced in October 2015 and amended in January 2017, and the agreement to divest certain Rite Aid stores to Fred’s Inc. that was announced in December 2016. Both of those agreements have been terminated, and WBA will pay Rite Aid the $325 million termination fee called for in their initial merger ­agreement.

The new transaction is subject to the expiration or termination of applicable waiting periods under the Hart-Scott-Rodino Antitrust Improvements Act of 1976, as amended, and other customary closing conditions. The initial closing of the new transaction is expected to occur within the next six months.

Upon the initial closing of the new transaction, WBA will begin acquiring the stores and related assets on a phased basis over a period of approximately six months, and it intends to convert acquired stores to the Walgreens brand over time.

“While we believe that pursuing the merger with Walgreens Boots Alliance was the right thing to do for our investors and customers, this new agreement provides a clear path forward and positions Rite Aid as a strong, independent, multiregional drug store chain and pharmacy benefits manager with a compelling footprint in key markets,” commented Rite Aid chairman and chief executive officer John Standley.

“The transaction offers clear solutions to assist us in addressing our pharmacy margin challenges and allows us to significantly reduce debt, resulting in a strong balance sheet and improved financial flexibility moving ­forward.”

Standley continued: “I would like to thank our entire Rite Aid team for their extraordinary efforts during this process and their tremendous focus on taking great care of our customers and patients. We have an outstanding team of associates and, with their continued support, we will work together to deliver a great customer experience, improve our business and deliver value to all of our stakeholders.”

WBA expects the new transaction to be modestly accretive to the company’s adjusted diluted net earnings per share in the first full year after the initial closing of the new transaction, and anticipates that it will realize synergies from the new transaction in excess of $400 million.

These synergies are expected to be fully realized within three to four years of the initial closing of the new transaction and derived primarily from procurement, cost savings and other operational matters.