Part one began in January, when Nutting took control of the organization from Kevin McClatchy. Seven months later, McClatchy announced that he would step down from his position as the team's chief executive officer at the end of the season, which set in motion a search process for a replacement.
And on Friday, phase three began, as Nutting now begins to further complete that transition by beginning the search process for a new general manager.
As Nutting spoke with reporters on Friday, it became increasingly clear that his search for a replacement CEO played a role in his decision to head in a new direction with the GM position that Dave Littlefield had held since midway through the 2001 season.
One thing that Nutting has determined is that it is not in the team's best interest to hire a president/general manager to handle both jobs. Instead, he firmly believes that there should be a distinct separation in the duties and the qualifications for each unique position.
"A GM really needs to be single-minded, focused in developing baseball operation, bringing in talent, player development, baseball operations, all the way to the Major League club," Nutting said. "The president is really going to be in charge of the entire operation. It's becoming increasingly clear to me that where we need baseball decision-making horsepower is right in that GM position. Increasingly, I see those two things as two distinct skill sets."
Nutting did not want to publicize who the Pirates have formally or informally talked with regarding the CEO opening. But he did say that, in those talks, different candidates emerged that he felt fit the baseball-minded mold of the GM position better than they would as a new team president.
As a result, the search for a new GM has somewhat informally already begun.
"We have looked at a variety of different structures through the process. And when it came to some of the candidates we have been looking at [for the CEO position], some of those excellently qualified names possibly fit best in that GM spot," Nutting said. "I've talked with lots of people throughout the industry -- senior executives, people in the commissioner's office who have talked about various potential names, and that has helped crystallize where some of these pieces may fit."
When Nutting began the team's CEO search back in July, he said that he hoped to name a new CEO by the end of the season, which now sits just over three weeks away. On Friday, he reiterated that that timetable has not changed.
He did, however, also emphasize that Friday's announcement did not mean that the naming of that new president is necessarily a decision that has already been made or will be announced in the next few days.
Ideally, the Pirates would like to have a president in place before the search for a new GM concludes. Doing so would allow the CEO to be an integral part of the hiring decision, as well as clarify what strengths would be needed in a GM to complement his skills.
"I think it's critically important that we get input from the president, as well for the GM," Nutting said. "That's a team that's going to have to work effectively."
Nutting was, however, quick to add that while ideal, that particular hiring order is not set in stone.
"You have to be careful not to put restrictions on any piece of the process," Nutting said. "I don't want to make anything absolute. Certainly that is one sequence that it could flow."
The decision for both hires lies solely with Nutting. He has been conducting a one-man search process to fill the CEO vacancy, and he will conduct this new search process in the same manner.
What has thus far been a nine-month transition will likely be concluded within the next month, and Nutting's decisions will ultimately drive the direction of a ballclub that has struggled for years. Nutting didn't shy away from acknowledging that, as he insisted that these two eventual hirings aren't going to be decisions that he takes lightly.
"There's nothing more critical than getting the right team in place," Nutting said. "This decision is one I need to take responsibility for. Frankly, these are decisions that I need to get right."
Jenifer Langosch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.