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Don’t you just hate when a perfectly good story isn’t allowed to breathe and develop into a total crapstorm at a nice even pace? Of course you do.

Thus, your hearts are heavy today at the news that Jim Harbaugh has thrown down in response to Sunday’s Chronicle story about him losing some veteran players with his corrosive personality. Through the auspices of Sports Illustrated’s estimable Michael Rosenberg, and likely initiated through Harbaugh’s agent David Dunn, Harbaugh told a version of his side, and it is as you might expect an indirect but fairly pointed knee to the nethers of the 49er hierarchy.

[RELATED: Harbaugh: No issues with 49ers, contract, Baalke]

It is a sure sign that he is not going to lay down and let the public debate be shaped solely by the company, and while you may argue here and there about specific points, you may not ignore the essential signal that this corporate relationship is regressing to the point where it almost certainly will not be repaired – maybe not even by a Super Bowl.

And it’s only March 4. Jeez, what’s the hurry, kids?

The nervous public truce, such as it was, was essentially broken when the Cleveland Browns made their half-hearted play at Harbaugh right after the NFC Championship game, news of which was breached during the NFL Combine – the first valuable use for the combine ever.

It has escalated since then, and the latest turn came when someone within the 49er hierarchy told The Chronicle’s Ann Killion that a number of players have wearied of the Harbaugh style, while still content to enjoy the wins and playoff runs.

[RATTO: Leak makes for tenuous marriage between Harbaugh, 49ers]

This hits Harbaugh where he lives – the locker room, and the field. So he decided to fight media with media, something he does only infrequently, and he decided to do with a national rather than a local media figure. Clever tactical thinking, to the nth degree.

“It's a principle to me that you never negotiate contracts in the press,” he told Rosenberg. “It doesn't benefit anybody to do it publicly. I'm making this exception in talking to you right now and saying I'm not trying to get more money for myself. But I make plenty of money. I have plenty of security. If we have the highest-paid assistant coaches in football, the best coaches in football, I strive for that. Guilty as charged there.”

So it begins. He doesn’t want more money (which is dubious, given that this story line has been out in the open for months and he hasn’t chosen to refute it until now), but he wants it for his assistants.

"(Defensive coordinator Vic Fangio) has not had a raise since he's been here,” Harbaugh said. “Focus on that.”

And who is in charge of assistant coach pay? Why, the general manager, of course. Trent Baalke. Who works directly under Jed York. Focus on THAT.

But let’s break this down further, not because there is a side to have, but to measure what’s not being said, and how it is the actual story.

“I see all these reports about how I want to be the highest-paid coach in football,” Harbaugh said. “They presume I covet some kind of extension. I have never said to anybody that I want to be the highest-paid coach in football. I have never said that to anybody -- my wife, my brother, my dad. I make plenty of money.”

The duty of negotiating the extension would be Dunn’s job. As Harbaugh’s agent, he drives some of the hardest bargains in the NFL. Harbaugh wouldn’t have to say it. Dunn would know to do so.

“The other one is that I want more power. I have never said that, nor do I want any more power than I have. I coach the team. I've told my owner I don't want any more power. I want to coach the team. And I've never told anybody else otherwise.”

Everyone agrees that Harbaugh wants to be the coach and not the general manager. But that’s not the debating point, and it never has been. It is whether he can work with Baalke, or whether he would prefer a general manager who would let him have what he asks when he asks for it. The power isn’t in the title; it’s in dictating to the titled.

Harbaugh deals with that by telling Rosenberg, “We're (he and Baalke) both demanding and we want to be accountable for ourselves, for each other. If you haven't had a brother, you probably don't understand the relationship between the GM and the head coach. We're partners on the same team. I have great respect for him. He works extremely hard at it and is very good at it. We are all part of a team. I believe in the structure we have. I don't want to change anything that we do in that regard.”

Oh, I think he does. I think that everybody who knows him thinks he does. Again, he doesn’t have to be the general manager to control the office, and a contract extension at significantly more money does that job as well as a new title.

And lots of brothers have gear-grinding relationships. Unlike brothers, though, this one isn’t cemented by blood. They don’t have to share tense Thanksgiving dinners, and Jed York doesn’t really have the moral authority that Jack and Jackie Harbaugh do.

So could Harbaugh leave after this year? Does he want to do? Has he thought about it?

“No,” Harbaugh said. “Zero opportunity or chance of that in my mind.”

“Yes,” says the logical mind. Of course he’s thought about the end game. You don’t get to be a coach of his stature without a gift for strategy, and that includes envisioning the end game.

As for the contract, he said, “I have never been a guy that wants to get extensions. If the guy at the top is getting extensions every year or two, it sends everybody else to the water cooler. The reason is, in any kind of budget, you have so much money for coaches. At some point it comes down to a pool of money for the coaches. When I started out, I was making $5 million. You run back for an extension, it shrinks the pool.”

No it doesn’t. Budgets change all the time, and flexibility is built into them all. A raise for Harbaugh most certainly would not come out of the coaching budget. Maybe at the University of San Diego, but not in the NFL. A Harbaugh raise wouldn’t come out of Greg Roman’s pocket. The budget would rise to accommodate the head coach’s raise, and the head coach could even negotiate raises for his assistants as part of his own extension. This argument is, at best, disingenuous.

But is this the right time to talk extension?

“I don't know,” Harbaugh told Rosenberg. “What I do know is this: I make plenty of money. And I don't do five times as much work as any other coach on the staff. I get paid extremely well. Jed York has always been square dealing with me. I don't think about that as an issue . . . I’ve seen it written like fact: 'Harbaugh wants to be the highest paid coach in football,’ or ‘desperately covets a new contract.’ For the record: I make plenty of money. I mean, plenty of money.’”

In order: Yes he does make plenty of money. His workload doesn’t preclude him getting more, or getting more for his staff. This negotiation isn’t about square dealing, it’s about more money. They’re ALL about more money.

And finally, while he derides the “Harbaugh wants to be the highest paid coach” and “desperately covets a new contract,” he simply repeated the same mantra, “I make plenty of money.” Which isn’t the same as, “I don’t want more money.” Like we just said a paragraph to the north, extensions are solely about more – time, and money. And when he was asked when the right time for an extension, he didn’t say, “At the end of the contract.” He said, “I don’t know,” which is code for “Yes I do know, and it’s now.”

In sum, Jim Harbaugh is asking for an extension, which is his right. That extension is for a lot of money, which is also his right. He believes he has leverage, which he does, though not as much as he would like in the short term, because leverage for an employee always comes down to leaving.

And has he thought about leaving? Yes, but not for the crummy old Browns job.

[RELATED: Jed York learns valuable lesson]

“There was never any opportunity to leave the San Francisco 49ers," he said. “If that existed, it existed in somebody else's mind, not mine. I am too fond of my team, the players, the coaches. I really feel like we have one of the best, if not the best organizations in football.”

Whose mind? Well, someone in San Francisco took the call from Jim Haslam. Use your own math on that.

And finally, that “It's a principle to me that you never negotiate contracts in the press” thing? For one thing, I thought he wasn’t renegotiating (well, that’s one cover story blown).

But for two, his chat with Rosenberg wasn’t about a new contract. It was about rebutting what he clearly sees as the 49ers' intention to use the media to their own ends. This was his opening response, and the exchanges will not get prettier unless and until someone backs down.

I wouldn’t bet any of Vic Fangio’s raises on that happening any time soon.