It was always going to be more than simply changing the nameplate on the door.

When Mark Shapiro was hired as the president of the Toronto Blue Jays at the end of August, replacing Paul Beeston, the move signalled a full-scale culture shift for a franchise that has done business essentially the same way since the earliest days of its existence.

True, the make up of ownership shifted over the years – from a three-way partnership of Labatt’s, Howard Webster and the CIBC, to Labatt’s alone, to the Belgium-based Interbrew, which swallowed up the Canadian brewer and the Jays along with it, to Rogers Communications, which jumped in at a time when not a lot of folks (at least in Canada) seemed particularly interested in buying the team.

But from the day that Beeston and Pat Gillick managed to oust the Jays’ original president, Peter Bavasi, in a kind of coup d’etat way back in 1981, things had worked pretty much the same way, even after Gillick moved on, and after Beeston did for a time before returning (during his time working for Bud Selig in New York he never gave up his office and secretary at the Rogers Centre.)

Among the Blue Jays’ current staff there is still direct lineage going back not just to the glory days of the late ’80s and early ’90s, but to that first April afternoon when Doug Ault briefly became a household name. Beeston dated back even farther than that – he was hired to look after the books as the team’s first employee.

And now, that’s over – which didn’t really sink in for Blue Jays fans until the announcement on Thursday that general manager Alex Anthopoulos had declined the owner’s offer of a five-year extension and would be moving on.

Anthopoulos was a product of that old culture (though he also chafed against it at times, and though he in fact began his career with the Montreal Expos.) It was within the Blue Jays organization that he learned the ropes, that he quickly rose through the ranks and that he was given an opportunity to run the team at a very early stage in his career.

Would he have become that guy somewhere else? Probably. Eventually. But the fact that Beeston gave him a shot after the firing of J.P. Ricciardi rather than going out and hiring a new general manager from elsewhere was a very Blue Jays thing to do. So was the fact that Anthopoulos was granted a significant degree of autonomy in running the baseball side of the business. There were payroll parameters, and occasionally Beeston or ownership intervened to push or block a trade or a signing. But beyond that, Anthopoulos could shape the organization as he liked, hire the field manager he wanted, and make whatever deals he could as long as he didn’t spend outside the bounds of his budget.

It wasn’t going to be like that anymore, and Anthopoulos knew it. He knew it as far back as last fall, when stories surfaced about the possible hiring of Dan Duquette or Kenny Williams as team president – both of them with baseball operations pedigrees. Maybe they could work something out, which allowed him to retain his autonomy, to retain the final say on personnel matters. But that would be a long shot, even if there was a pre-existing relationship.

Shapiro he didn’t know at all, and the former Cleveland Indians GM and president came from a different place, where they did things differently, where there were different loyalties, where there was a very different history. He was hired by Rogers (apparently with the blessing of new baseball commissioner Rob Manfred) to shake things up, on some level to make them better. He is by all accounts a detail person, a memo person, a meeting person – none of which are labels anyone would apply to Beeston. He will make the Jays more button down, more efficient, more modern, and more a part of a larger communications company.

That’s certainly not all bad – and there are people inside the organization who have been whispering for some time that it badly needed an injection of fresh air. But it was always going to be traumatic and cause collateral damage. Anthopoulos’s departure is just the beginning of that, though of course it’s the part that will resonate most directly with the fans.

Anthopoulos had become a folk hero here. By season’s end, most of his detractors had fallen silent and he had become as popular with the fan base as any of his players. They liked the results on the field. They thrilled at the return to the post-season. But they also picked up on the fact that he was one of them, not just as a Canadian, but as a guy who loved the game, who wasn’t good enough to play it at a high level, but who got to live out the dream of every baseball geek and put together a team that almost made it to the World Series.

He could have stuck around and taken the money and the term, and if he had, no one would have blamed him. But he knew better than anyone that it’s a different place now, one where he wouldn’t feel so at home, and one where he wouldn’t have the final say.

A worse place? Well, let’s wait and see what happens.