For the previous 117 years, there had been an independent contractual relationship between Major League Baseball and Minor League Baseball (formally known as the National Association of Professional Baseball Leagues, or the “National Association,”, for short). Minor League Baseball had a separate office and President. Before the Professional Baseball Agreement between Major League Baseball and Minor League Baseball expired on September 30th, 2020, there were long and contentious negotiations between both sides about how their relationship was going to proceed, if at all.
Baseball America has a nice timeline on the negotiations and the issues involved in this article here.