Farrell officially became the new Red Sox manager on Sunday afternoon, when the two clubs agreed to terms on compensation. Veteran infielder Mike Aviles heads to Toronto as part of the deal, while right-hander David Carpenter goes to the Red Sox along with Farrell.
The move comes after weeks of speculation -- and even dates back to 2011, before Boston settled on the controversial Bobby Valentine as their manager, and who was recently let go by the ballclub after a 69-93 season.
"As John explained it to me, this was a dream job for him," Blue Jays general manager Alex Anthopoulos said on Sunday. "It was an opportunity he really wanted to pursue. [We] felt if there was a deal that could make sense for our club as well, we were going to go ahead and try to complete that."
Farrell, who spent four seasons as Red Sox pitching coach, from 2007-10, had long been considered the heir-apparent to Terry Francona in Boston. That led to plenty of rumors about Farrell's availability last offseason following Francona's departure and ultimately prompted the Blue Jays to institute a club policy which prohibited employees from departing for other organizations in lateral moves.
Despite the change in philosophy, speculation regarding Farrell's ties to Boston resurfaced in August. The talk continued into the offseason, but Anthopoulos remained steadfast in his claims that Farrell would remain the manager in Toronto.
All of that changed when the two men sat down together shortly after the season ended. Following the Canadian Thanksgiving on Oct. 8, Farrell informed Anthopoulos that he would like to join the Red Sox if an opportunity presented itself. At the time, no communication had taken place between the two clubs, but that also would quickly change.
Within the next day or two, Red Sox owner John Henry placed a call to Blue Jays president Paul Beeston. The initial groundwork was laid. It was up to Anthopoulos and Boston GM Ben Cherington to settle on the appropriate compensation.
"My focus at that time was completely on the roster," Anthopoulos said. "We have a lot of work to do on the roster, starting rotation, and that's where it needed to be. There was no plan whatsoever, it was 100 percent, John was going to be the manager for 2013, we were going to continue to discuss things like we always do. Finalize staff, finalize roster, talk about offseason needs, things like that.
"But then, ultimately, when we finally discussed the Boston scenario and that it was a distraction which came up ... he told me he wanted to pursue it and it was something that he really wanted. Ultimately, we both agreed that we couldn't wait forever and if there wasn't any movement within a few days we were going to put it to bed and we were going to move forward."
But the movement did occur. Now the Blue Jays find themselves in an awkward position of needing to fill a managerial vacancy, despite having not prepared to tackle that task this offseason. One thing working in their favor is that Anthopoulos conducted a similar search just two years ago and several of those candidates are still available.
Sandy Alomar Jr. finished as a runner-up to Farrell in 2010 and could receive consideration this time around. Alomar Jr. was unsuccessful in his quest to be hired as manager in Cleveland just a few weeks ago and has close ties to Toronto, where his brother, Roberto, currently works as a special assistant to Beeston.
Tim Wallach, DeMarlo Hale and Manny Acta could also enter the mix. Anthopoulos said he doesn't expect the search to drag on like it did two years ago, but also couldn't provide a timeline on when something might get done.
Even though Farrell essentially asked for an out, Anthopoulos said both parties were fully prepared to move forward if a trade with Boston could not be worked out. The fourth-year GM dismissed talk that their professional relationship had soured and said plans for the 2013 campaign had already begun.
What was most upsetting to Anthopoulos was not that Farrell never really appeared to sever his ties with the Red Sox, but instead the reports that came out in the weeks and months leading up to his departure. A recent media report, which suggested Farrell wanted potential Hall of Famer Omar Vizquel released in July, was the biggest bone of contention.
"I think for me with this whole process, what's more disappointing to me is that there was so much false information put out there," said Anthopoulos, who declined to get into specifics, but appeared to be pointing the finger toward Boston. "I read something the other day that supposedly John asked for us to release Omar Vizquel in July. Did not happen, 100 percent false, not one ounce of truth to it.
"A transaction like this, you'd love to see it be a little bit more smooth. It just seemed like a lot of the things that came out didn't come out from the Toronto media, it seemed like it was coming out of the Boston market. That's not to say people didn't rely on their own sources, but it's unfortunate that a lot of false things were being put out there."
Aviles gives the Blue Jays another option up the middle as the club heads into an offseason of uncertainty. Kelly Johnson, who was Toronto's everyday second baseman in 2012, is expected to leave as a free agent, while veteran Yunel Escobar has been frequently mentioned as possible trade bait.
The 31-year-old Aviles, along with top prospect Adeiny Hechavarria, provides the club with potential in-house replacements. That depth also could allow the Blue Jays to focus more of their attention on providing some much-needed upgrades to their starting rotation.
Farrell's departure comes after two disappointing seasons in Toronto. The Blue Jays did manage to finish at .500 in 2011 (81-81), but they regressed this past season, thanks in part to a series of devastating injuries and sub-par years from previously established performers.
Even though things obviously didn't end up working out, Anthopoulos said he has no regrets over making Farrell his first hire as manager.
"You're never going to get me on a conference call ranting and raving, it's just not my style," Anthopoulos said. "John gave everything he had, he worked incredibly hard from start to finish. He never let up his focus, always remained on the job. There's no question, you'd prefer that something like this doesn't happen, but I think it's a really unique set of events.
"I understand but, it doesn't mean I'm happy about it. It doesn't mean this is the way I would have drawn it up. But the facts are the facts and we need to do what's best for the organization. We need to move forward."