New York Mets general manager Billy Eppler resigned Thursday amid a Major League Baseball investigation into his use of the so-called phantom injured list, sources told ESPN.

The practice of placing players on the IL with fake injuries is a long-accepted but ethically murky part of baseball, according to sources. Teams will ask players -- often struggling and on the fringe of a roster -- to accept an IL placement even when capable of playing, sources said. The player gains the benefit of service time, a major league salary and retaining a spot on the team's 40-man roster, while the team retains the player amid a potential 26-man roster crunch.

MLB has investigated past phantom IL placements, sources said, though any punishment from those inquiries is unclear. Teams are expected to offer documentation -- as well as a doctor's approval -- to support injury claims.

Eppler's resignation, which came three days after the Mets introduced David Stearns as president of baseball operations, stunned the baseball world. Eppler, 48, was expected to stay on despite owner Steve Cohen officially handing Stearns control of the team's baseball operations department this week. In a statement, Eppler said: "I wanted David to have a clean slate and that meant me stepping down."

Later, after the New York Post first reported the investigation into Eppler, multiple heads of baseball operations departments told ESPN they would not consider phantom IL use an offense worthy of resignation, though they acknowledged it could signal a crackdown by the league on the practice.

The Mets this season placed 25 players on the IL a total of 28 times, according to ESPN Stats & Information. That ranked 16th among MLB teams. San Francisco, with 46 IL placements, was first, just ahead of Cincinnati (45) and the Los Angeles Angels (42). Houston had the fewest players (14) hit the IL, with Cleveland (17) and Seattle and Arizona (18) staying relatively healthy.

Eppler is now the second top Mets official to leave the organization in the past week, after the team fired manager Buck Showalter. The changes follow one of the most disappointing seasons in franchise history. The Mets entered the year with the largest payroll in MLB history and World Series aspirations. They ended it having dealt nearly a quarter of their major league roster at the trade deadline and finishing 75-87, fourth in the National League East division and 29 games behind first-place Atlanta.

Eppler was hired in late 2021 after the Mets fired Zack Scott, their interim GM, who had been charged with DWI but later was found not guilty. Scott replaced Jared Porter, who was fired 38 days after being hired following an ESPN report that he had sent explicit text messages to a female reporter.

Stearns, 38, joined the Mets after seven seasons running the Milwaukee Brewers that included four playoff appearances. While his arrival in Queens had been long expected, there was no indication in his opening news conference three days ago that Eppler would not be part of the team's infrastructure.

Eppler's first season with the Mets, whom he joined after five years as Angels GM, wound up with 101 wins -- and an ignominious loss in the wild-card round. While he warranted praise for an offseason in which he had signed ace Max Scherzer and acquired steady starter Chris Bassitt, Eppler's lack of urgency at the trade deadline led to a trio of dud moves, as the team added only designated hitter Daniel Vogelbach, first baseman Darin Ruf and outfielder Tyler Naquin.

The Mets' spending spree over this past winter brought back closer Edwin Diaz and center fielder Brandon Nimmo while adding future Hall of Famer Justin Verlander and Japanese star Kodai Senga. Diaz's season-ending injury in the World Baseball Classic cast a pall on this season, and by the time the deadline rolled around, the Mets punted, trading Scherzer to the Texas Rangers and Verlander to the Houston Astros.

New York enters a seminal winter, with two-way star Shohei Ohtani -- whom Eppler signed as GM of the Angels -- reaching free agency and the Mets mulling the future of first baseman Pete Alonso, who is a year away from free agency and hired agent Scott Boras this week. They also will continue looking for a manager after the firing of Showalter, whom Eppler hired in December 2021.