In the coming days and maybe weeks we’re going to see some sort of word battle between people from the Jim Harbaugh camp, and those from the San Francisco 49ers, speaking or leaking on behalf of Jed York and Trent Baalke. Whatever is being said, it’s not hard guessing what happened behind the scenes.

Obviously, it’s all speculations, but if there was something really big and unethical that Jim Harbaugh did to get him to generate so much hate and tension between himself and the front office, we would have heard by now. Maybe he did lose some faith of players in the locker room, but many players and coaches weren’t exactly loved by others and managed to do great things. Harbaugh wasn’t let go (and left himself) because the front office didn’t like what was going on between him and his players.

Jim and I have had conversations since he’s been here, but in the last, probably two or three weeks, we’ve talked about it, we’ve talked about different scenarios, different opportunities, and ultimately we just came to the conclusion that it was best for us to go in different directions. Again, we’ve had philosophical discussions and when we sat down we just couldn’t come to a place where we thought moving together was the best for either party. This wasn’t us saying, ‘Jim, you’re fired, you’re not here anymore.’ This wasn’t Jim saying, ‘I don’t want to be there, I’m leaving.’ It was a discussion that took place over a decent amount of time to figure out what’s best for everybody involved. It wasn’t an easy conclusion for anybody but that’s where we ended up. It was the right decision for both parties at the time.

The most obvious reason is often the real one, and in this case, it’s York and Baalke hating to see Harbaugh assume control and get all the credit for the 49ers becoming one of the best teams in the NFL from the moment he took charge of them. Sure, GM’s and sporting directors who make draft picks have a big part of the success and failure of a team, but it’s hard to think of great teams that didn’t have very good head coaches. That might be the most important ingredient and building block for NFL teams.

Two other strong rumors might hint at these ‘philosophical differences’ but it’s obviously more than that. Rumor has it (maybe coming from the Harbaugh camp) that he wanted Ray McDonald suspended from the moment legal problems surfaced. Bulking the trend in the league during those weeks, the 49ers stuck with McDonald until that more allegations came later in the season. By coincidence, by the time he was let go the Niners were out of the playoff, so maybe that was why he was really released.

Another thing that makes sense is the whole Greg Roman and assistants issue. The 49ers gave Harbaugh plenty of assistants on offense but that aspect deteriorated this season, along with Colin Kaepernick having a very rough second season as a starter. A lot of fingers were pointed at Greg Roman. Did Baalke ask Harbaugh to fire him (the contract Harbaugh was on gave him full control of his assistants) and offer a contract extension worth $7.5 million in return? That doesn’t sound too ludicrous, but again, just rumors.

The Niners’ brass was on a collision course with Harbaugh the moment they didn’t give him the contract extension he wanted. All year long the rumors and bad feelings crept and played a part in this team’s demise, which might be temporary, but considering that big chunk of key players from the last four years of success might be leaving for good (Justin Smith, Frank Gore, Mike Iupati, Ahmad Brooks, Perrish Cox and others), letting the rift between them turn from personal into professional might turn out to be a huge mistake.

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