How the 49ers plunged from greatness to dysfunction in one year 

Even now, the odor of self-sabotage lingers. Something stinks in Santa Clara, and it isn’t the fertilizer in the 27,000-square-foot, solar-powered rooftop garden at Levi’s Stadium. Rare is the sports franchise that runs off a wildly successful coach, one armed with merely the best three-year start in NFL history, because the people in charge think they can do better.

Such is the bizarre, staggering tale of the 49ers and their ugly divorce from Jim Harbaugh. Usually, on-field prosperity trumps any political tug-of-warring behind the scenes, realizing that many of football’s most triumphant coaches — from Lombardi to Parcells to Belichick to Walsh — have won multiple championships with complex personalities. Whatever Harbaugh was doing to distract or disrupt the daily mission, it’s hard to believe that could overwhelm three consecutive NFC title-game appearances.

Somehow, CEO Jed York and general manager Trent Baalke couldn’t fix the issue, maybe because they didn’t want to. It hardly seems coincidental that the team’s fortunes subsequently have regressed with frightening speed, first with an 8-8 season, then with Harbaugh’s departure to the University of Michigan, then with the peculiar in-house hiring of unproven Jim Tomsula as head coach, then with the mass exodus of quality leaders and cornerstones such as Patrick Willis and Frank Gore. When linebacker Chris Borland made his groundbreaking decision to retire at age 24 rather than risk a career of head injuries, the 49ers seemed as cursed as they are chaotic.

For three years, no NFL team was shinier. Harbaugh reminded everyone of this at every turn with almost cornballish enthusiasm. “Who’s got it better than us? Nooo-body!” the hyperintense leader would shout as his players echoed the affirmation. He was the first NFL coach to win five playoff games in his first seasons, an astounding turnaround from a team that had won 44 percent of its games the previous three years. The future looked wonderful. The Niners were a 21st-century San Francisco treat, and there was a flashback symmetry to the early days of Joe Montana and Bill Walsh, even to Dwight Clark and The Catch. What could go wrong?

Everything.

At some point, York and Baalke stopped listening to Harbaugh. Never mind that neither had been responsible for many of the building blocks that helped create the success — Willis, Gore, Vernon Davis, Justin Smith, Joe Staley — and that most league insiders cited Harbaugh as the driving force behind the surge. They were eager to move on from him, disregarding that the 49ers had missed the playoffs the previous eight seasons before his arrival. The ever-burgeoning divide precipitated a breakup that York summed up by saying the team and Harbaugh had “mutually parted.” Harbaugh later told a Bay Area columnist that he felt the front office abandoned him, saying, “I was told I wouldn’t be the coach anymore. And then ... you can call it 'mutual.' I mean, I wasn’t going to put the 49ers in the position to have a coach they didn’t want any more. But that’s the truth of it. I didn’t leave the 49ers. I felt like the 49er hierarchy left me.” It was typical of the double-talk that started a year earlier when mysterious whispers ended up in news stories from unnamed organization sources — almost all of it anti-Harbaugh.

Gleefully, Harbaugh landed on a pile of cash in Ann Arbor as Michigan’s new head coach. The 49ers launched into a free-fall, with few beyond earshot of Levi’s Stadium believing the team is better off without him. Where the 49ers find themselves now is difficult to fathom. It’s a long, long way from Jan. 19, 2014, when a last-second interception against the Seattle Seahawks in the NFC championship game prevented the 49ers from a second straight Super Bowl appearance.

But, hey, at least York and Baalke won the power struggle with Harbaugh. Upon closer inspection, however, that outcome has all the markings of a Pyrrhic victory. Harbaugh, all three of his coordinators and most of the other assistant coaches from last season are gone. So are numerous key players, including several whose 49ers tenure goes back as far as a decade.

If nothing else, credit the 49ers for making the Raiders, who had the dysfunction market cornered, seem like the most stable NFL team in the Bay Area for the first time in years.

York and Baalke claim the goal is to win a Super Bowl each year. It wasn’t until Harbaugh arrived that the 49ers made headway toward that end after a long dry spell. Also, plenty of that success can be attributed to players acquired before Baalke was promoted to general manager in 2011 and York took the reins of the franchise.

Harbaugh had no NFL head coaching experience when York hired him away from Stanford in 2011. Harbaugh, York and Baalke grew into their roles simultaneously. For a while, they seemed like the perfect troika.

In Harbaugh, York and Baalke had a coach willing to stand in the spotlight and absorb the heat while they did their thing in relative peace. There isn’t anywhere to hide now.

York and Baalke created this situation, which many consider a mess. Make no mistake; This is what York and Baalke had in mind all along. The 49ers are going to win, the thinking goes, regardless of who oversees the players.

Even if that coach isn’t known by many outside the 49ers headquarters. This situation is eerily reminiscent of what the Raiders endured the last time they enjoyed sustained success.

In 2001, after back-to-back playoff appearances, then-Raiders owner Al Davis traded coach Jon Gruden to the Tampa Bay Buccaneers for four draft picks and $8 million, ostensibly because Gruden had become the face of the franchise. In other words, Gruden had become more revered than Davis.

Just like that, Gruden was jettisoned after four seasons. The Raiders went to the Super Bowl their first season without Gruden, who, coincidentally, coached the Buccaneers to a lopsided victory over the Bill Callahan-coached Raiders in that Super Bowl.

The Raiders haven’t had a winning season since 2002. Time will tell if the 49ers are able to avoid a similar fate. Safe to say, the 49ers are off to a rather inauspicious start in the post-Harbaugh era.

A widespread search for a replacement for Harbaugh yielded Tomsula, the 49ers longtime defensive line coach and someone whose head coaching experience consisted of one NFL game as an interim head coach and a brief stint in NFL Europe.

Tomsula very well might develop into a top-notch head coach. Good luck finding someone willing to consider him an upgrade over Harbaugh, though. The move also did little for fans by way of inspiring confidence in York and Baalke as the unquestioned decision-makers.

Former NFL MVP Rich Gannon, who starred for the Raiders and now broadcasts NFL games for CBS, said the 49ers have “a lot of work to do” if they’re going to bounce back from last season’s .500 finish and a disastrous offseason. Losing Harbaugh, defensive coordinator Vic Fangio and offensive coordinator Greg Roman is a crushing blow, Gannon said.

Throw in the departures of Willis, Gore and guard Mike Iupati, and Tomsula has more to worry about than figuring out a way to get past the Seahawks. The situation become futher complicated by the possible exits of free agent wide receiver Michael Crabtree and defensive lineman Justin Smith, who hasn’t decided if he wants to return for a 15th season. “It’s just devastating to lose those players … not only in terms of their production and their consistency, but their leadership in the locker room,” Gannon said. “That’s going to be a real challenge.”

It’s going to be just as much of a challenge for York and Baalke to convince people that they are as vital, if not more so, to the 49ers success than Harbaugh proved during his four-year tenure.

Gannon, who played for the Raiders during Gruden’s final three seasons there, said the key to the 49ers short-term success is how well quarterback Colin Kaepernick plays next season. “He’s got to grow up,” Gannon said in reference to Kaepernick’s on-field performance. “He’s got the contract and the physical skills, but he’s got to play better.” Gannon called Kaepernick’s season last year a “very disappointing” one. For that to change, he said, Kaepernick needs to improve his mechanics, his accuracy and his decision-making.

Ultimately, Gannon said, it’s the teams with the stability that enjoyed sustained success. He called the Patriots, Packers and Ravens the exceptions. What the 49ers are going through isn’t all that unusual.

“That’s the nature of our business anymore, with free agency, players coming and going, too many owners who lack patience and fire coaches after a year or two … There are very few teams that have sustainability.”

The 49ers had it for four years. It won’t take long to find out if York and Baalke threw it all away or if they’re truly smarter than they are being credited. If they aren’t, who will have it better than the 49ers?

Evvvvv-eryyyyy-body.

Staff writer Paul Ladewski contributed to this article.

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Steve Corkran

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