San Francisco 49ers defensive backs L.J. McCray (31), Keith Reaser (27) and Jaquiski Tartt (29) during an NFL football mini-camp in Santa Clara, Calif., Wednesday, June 10, 2015. (Jeff Chiu/AP Photo)

San Francisco 49ers defensive backs L.J. McCray (31), Keith Reaser (27) and Jaquiski Tartt (29) during an NFL football mini-camp in Santa Clara, Calif., Wednesday, June 10, 2015. (Jeff Chiu/AP Photo)

The wreckage in Santa Clara

This feels like one of those post-apocalyptic movies where Colin Kaepernick, played by Will Smith, surveys the devastation and says, “WTF?” No one is entirely certain what happened to the San Francisco 49ers as we once knew them, including the fact they’re no longer remotely near San Francisco, having moved 38 miles south to an uninspiring blob wedged between freeways, a convention center, an amusement park and a green space where kids are upset at CEO Jed York for trying to turn soccer fields into VIP parking.

It’s as if three NFC title games never happened those three Januarys, that the Niners never played in a Super Bowl in which they were five yards — and some creative play-calling — from a world championship. Hell, it’s as if Joe Montana and Jerry Rice never happened, Bill Walsh and George Seifert never happened, “The Catch” and Candlestick never happened, John Brodie and Kezar never happened. What was lost in the move to Santa Clara won’t ever be recaptured, and the result is something unrecognizable and beyond disturbing for a myriad of perplexing and stupid reasons.

The franchise went from having a robust NFL identity and brand under Jim Harbaugh — rugged, sturdy, prepared, always competitive down to the black shoes — to … what, exactly? Losing Harbaugh, as the world outside of 4900 Marie P. DeBartolo Way knows, was an act of corporate foolishness. It implicated York, whose full-on beard now makes him look 28 instead of 23, as a boss who preferred to indulge in office politics and fire the feisty Harbaugh rather than try to smooth his rough edges and make his considerable coaching talents work in the bigger paradigm. Harbaugh is not the first football coach who is difficult for others to deal with — Bill Belichick, Bill Parcells and Vince Lombardi come to mind — but he also was winning hardware and quickly transforming the 49ers from a laughingstock to an annual force. It was incumbent upon York, as the big exec, to manage the creative tension and maintain a successful formula.

Instead, he joined hands with general manager Trent Baalke to purge the “monster.” They’ve yet to explain why Harbaugh was so divisive, and while I hear that he sometimes stomped around the football building like a frenetic freak, why do you think the 49ers were a top-five operation and playing in huge games? Because he’s a frenetic freak. Now he’s at Michigan, where they’ll gladly deal with his personality quirks and daily khakis if he beats Urban Meyer a few times. Apparently, beating Pete Carroll a few times wasn’t enough for York and Baalke, which is sad.

Now the 49ers are left with Jim Tomsula, a career assistant who once was a head coach in Europe and wasn’t nearly as qualified for this job as Stanford’s David Shaw — gee, Jed, no moving expenses — or respected defensive coordinator Vic Fangio, who fled to Chicago. And they are left with a roster so mind-bogglingly depleted by retirements, defections and trades, it’s fair to ask if the turnover is unprecedented in moden football annals. In just a year, the 49ers have nose-dived from a Super Bowl-type operation to a team that may be lucky to win six games in the league’s most competitive division.

But at least everyone seems to be getting along down there.

After all, they have only each other.

What does Tomsula like about the team he inherited?

“The team aspects of it. The way everybody’s working together,” he said. “The way these guys talk to each other. The way these guys treat each other with the dignity and the respect that everybody deserves. The way they treat everybody around the building. And just the way they’re doing it together.”

Last we looked, “Kumbaya” alone doesn’t win football games. If we can commend the 49ers for trying to cleanse their public image after 11 arrests among seven players since 2012 — they particularly look prudent for dumping Ray McDonald before he was arrested again in late May — their emphasis on behavior is only part of any rebuilding equation. Tomsula, a simple guy from western Pennsylvania, is trying to keep things simple as it comes to character, saying, “I’m not really big into don’t do this, don’t do that and 100 things. We’ve got one rule: Do right. Basically, the only thing I have is have fun, be smart and be safe. That’s where we’ve got to go.”

The greater puzzle is infinitely more complicated than that. The 49ers didn’t just lose an abundance of players. They lost leadership cornerstones such as Frank Gore, Patrick Willis and Justin Smith, who made 17 Pro Bowls. They lost 24-year-old Chris Borland to retirement, a decision so profound that it prompted a national commentary about young players prioritizing long-term health over money, and then they lost 25-year-old right tackle Anthony Davis for the same reason. Willis, too, interrupted an outstanding career for quality-of-life reasons, and when management allowed the likes of Gore, guard Mike Iupati and cornerbacks Perrish Cox and Chris Culiver to leave as free agents, NFL people were left to ask the same question: What on earth is happening in Santa Clara that would lead to such volatility?

Like any other American workplace, the direction — or lack thereof — comes from on high. Joe Lacob turned around the Warriors with vision and bold decisions. Larry Baer helped build a mini-baseball dynasty in China Basin by hiring astute baseball people and trusting their wisdom. York? He had a wonderful thing going, got his new stadium built in Silicon Valley, then couldn’t sustain it. It’s hard to believe he’s the nephew of the dynamic owner from the team’s former glory days, Eddie DeBartolo Jr., proving that a family tree doesn’t necessarily produce ripe fruit. At some point, the day may come when John York and Denise DeBartolo York tell their son that he can’t run the shop any longer.

That day may come this winter, if the record is 6-10 … or worse.

The 49ers won’t completely fall apart, not after adding an explosive deep threat in Torrey Smith, a still-dangerous Reggie Bush as a backfield complement to hard-charging Carlos Hyde and defensive end Darnell Dockett. They also welcome back NaVorro Bowman, whose ravaged knee in the 2014 NFC ttile game seemed to launch the franchise free-fall. But is Kaepernick really going to be a more polished, accurate and disciplined performer because he worked with Kurt Warner in the offseason?

If he’s really more mature, why is Kaepernick still sending out dumb tweets? With the mass exodus of so many respected veterans, doesn’t he, as the quarterback, have to be the vocal leader?

“I don’t think this team needs that to be vocalized,” Kaepernick said. “I think everyone realizes the players we have lost and that the players we have here are very capable of stepping in and being impact players.”

“Colin just has to be Colin,” Tomsula said. “Colin’s good. I mean, people lead in different ways. Some people talk a lot, some people don’t. Some people speak volumes without ever opening up their mouth. Be a great teammate. The things he’s doing right now, just for the record — who he is and what he’s doing — I’m his No. 1 fan.”

Yes, they are fans of each other in Santa Clara. That’s nice, because it’s a lost cause trying to find many others who believe in the 49ers, whoever and whatever they’ve become.

Jay Mariotti is sports director and lead sports columnist at the San Francisco Examiner. He can be reached at Read his website at BelichickBill ParcellsBill WalshColin KaepernickDavid ShawFrank GoreGeorge SeifertJed YorkJerry RiceJim HarbaughJim TomsulaJoe MontanaJohn BrodieJustin SmithKezar StadiumMarie P. DeBartoloPatrick WillisPete CarrollSan Francisco 49ersSanta ClaraTrent BaalkeVic FangioVince LombardiWill Smith

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