On Tuesday, Hoyer rejoined the architect of that '04 team, Theo Epstein, along with Jason McLeod, another key part of Boston's success, to become the Cubs general manager. Hoyer inherits a team that has not won a championship since 1908, the longest drought in professional sports.
"That challenge is part of the lure of the job," Hoyer said Tuesday at his introductory news conference at Wrigley Field. "One of my greatest moments is 2004. It transformed an entire region. I don't act like this is a small task [with the Cubs] -- it's an incredibly big challenge. But that's part of the fun. If it wasn't that, I certainly wouldn't be here."
The main reason Hoyer left his job as the Padres GM and McLeod said goodbye to San Diego to head scouting and player development in Chicago is Epstein, who was named president of baseball operations last week.
Having the three together again as they were in Boston has been compared to a reunion tour. Epstein and McLeod are musically inclined, while Hoyer says he'll try to play the triangle. OK, who's the smartest of the three?
"Theo," Hoyer said without hesitating. "It doesn't matter who else is in the room. I've worked with him for a long time and he is as down to earth a guy as you're going to find. When he turns it on, it's pretty clear he has a gear that the rest of us don't have. It's impressive. It's fun to be around."
Would Epstein have left Boston if he couldn't bring Hoyer and McLeod with him?
"This job got a lot more attractive once it became clear that I had a chance to land both of these guys," Epstein said. "These days in baseball, it's difficult, if not impossible to go someplace completely on your own. I'm the first to say there are great people here [with the Cubs] and I believe it more now.
"Trust is so important in baseball, and it's something I recommend to anyone who changes organizations," he said. "Bring someone along who you have history with and who you can trust implicitly right from the beginning."
Hoyer worked with the Red Sox for eight of Epstein's nine years there as GM, and the trio combined on two World Series championship teams in 2004 and '07.
"Jed has been general manager for two seasons now, but he's been thinking like a GM for a long time," Epstein said. "He has a deep understanding of the baseball landscape on and off the field. He's long been my right hand on Major League transactions, including moves that have directly led to two World Series titles."
Hoyer, who turns 38 in December, leaves the Padres after two years as the general manager to become the Cubs' 14th GM, replacing Jim Hendry, who was dismissed in August. Although his time in San Diego was limited, Hoyer left his mark.
"Thanks to Jed Hoyer's leadership, we are in a far better position to win consistently in the future than we were two years ago," Padres CEO Jeff Moorad said on Monday.
The Cubs offered Hoyer a five-year contract, which the Padres declined to match.
To be determined is compensation for both the Padres and Red Sox. The Cubs are expected to send a Minor League player to San Diego for Hoyer. MLB Commissioner Bud Selig had set Tuesday as the deadline for the Red Sox and Cubs to settle compensation for Epstein, but the two teams were expected to get an extension.
Bush, who took over as the Cubs' interim general manager after Hendry was dismissed, will remain as an assistant to the general manager.
Epstein said Hoyer will handle the Major League club's day-to-day responsibilities, plus have significant duties throughout baseball operations. McLeod will be the "go-to guy" for scouting and player development.
"This is more than a one-person job," Epstein said. "It's not even close to being a one-person job. The thought is, with the three of us in the trenches along with Randy, Tim [Wilken] and Oneri [Fleita], that maybe we can get to where we want to go, which is to build a foundation of sustained success a little quicker than if it's just one or two people trying to get it done."
McLeod, who turns 40 this month, inherits scouting director Wilken, who is signed for next year, and Fleita, who was the Cubs' player development director, and given a four-year contract extension. In the next few days, McLeod will meet with the two to go over every player in the Cubs' system.
"Jason is a terrific manager of people," Epstein said. "He challenges his staff and demands excellence, but at the same time inspires loyalty. He will supervise the amateur scouting and player development operations, connecting both departments under a single, shared philosophy."
McLeod worked for the Red Sox and Epstein for six years, joining Boston in 2003. His first Draft with the Red Sox produced '07 American League Rookie of the Year and '08 AL Most Valuable Player Dustin Pedroia.
The three may believe in the importance of player development but don't think Epstein is bringing Hoyer and McLeod simply because he wants "yes" men on his staff.
McLeod recalls a huge argument they had preparing for the 2005 First-Year Player Draft regarding pitcher Clay Buchholz. Epstein liked the right-hander; McLeod loved him.
"We had an epic argument," McLeod said. "He threw something in the Draft room. Everyone is staring at me in silence and I said, 'Let's take a break.'"
The Red Sox did take Buchholz in the first round.
"We debate quite a bit," Hoyer said. "One of the beauties of baseball is people like to debate it, people like to argue about it."
They'll argue and present their sides, but in the end, the goal is to reach a consensus.
"It's all about reaching the right decision for the Cubs, that's the most important thing, and debate is certainly part of that," Hoyer said.
And now, the three will get to work in Chicago.
"We have an opportunity to do something special for a special franchise," McLeod said.
Carrie Muskat is a reporter for MLB.com. She writes a blog, Muskat Ramblings, and you can follow her on Twitter@CarrieMuskat. This story was not subject to the approval of Major League Baseball or its clubs.