San Francisco 49ers owner Jed York speaks at the 2012 groundbreaking on the construction site for Levi's Stadium. Jeff Chiu/AP Images

SITTING AT HIS desk at the 49ers' Silicon Valley headquarters, the din of a nearby construction project almost 20 years in the making reverberating into his second-floor office, Jed York holds two cuff links and begins to cry. He catches himself, though, his eyes red and glassy. He always catches himself. York -- by title the 49ers CEO, by inheritance the owner, by his own characterization the steward -- isn't a crier. He's an almost crier, and he seems to almost cry when talking about two things, usually when they intersect: his family and his stadium.

His family is both iconic and controversial in the Bay Area, a mixed legacy that enriches and burdens him. York is 33, and though he was born into one of America's richest families, the DeBartolos, he has scars. He feels deeply the pain of public humiliation for which he bears no fault but aches to fix. He carries himself with a self-awareness that is rare for an owner. He gives away tickets to games at NinersFanContest. During league meetings, while many owners enlist a flack to carry their ballot to a box, York always delivers his personally. He gives his employees the best rooms at hotels, even if it means he stays in one with two twin beds. He is grateful for his job because he's seen how fast it can all slip away.

His stadium is under construction, a skeletal shell just 14 feet away from the 49ers' offices. It is already famous in the stadium world for what it will be: state of the art, green and wired, of Silicon Valley as much as it is in Silicon Valley. Levi's Stadium is its official name, but locals call it the House That Jed Built, a 68,500-seat miracle that will open next fall.

A miracle. It's strange to ascribe that term to a $1.3 billion building. But it fits. This particular stadium is being constructed in a region surrounded by cash-strapped counties, in a state that hasn't built a pro football venue in almost 50 years. It will open a year ahead of schedule. It will not only host the 2015 Super Bowl but house a Super Bowl contender, only four years after the 49ers were as irrelevant as the hopes for a new stadium were dismal. But beyond all that, the sharp clap of steel on steel emanating into York's office represents a wrong that he has spent years trying to right. The toll of that battle bubbles up in seemingly innocuous moments, such as when he opens a little box, colored 49ers scarlet, and tells the story of two cuff links.

Gold and weathered and shaped like footballs, engraved with a silhouette of a miner and the words 49ers Football, the cuff links once belonged to a woman named Josephine Morabito, whose family founded the team. In 1977 she gave them to Eddie DeBartolo -- "Uncle Eddie" to York, "Mr. D" to his players, the oldest son of Edward Sr., the late billionaire inventor of the modern mall -- after he purchased the team. Not really a cuff link guy, DeBartolo wore them only once, on Jan. 10, 1982, the day Dwight Clark made The Catch to send the Niners to their first Super Bowl. That was the beginning of the rise before DeBartolo's fall.

York skips forward to this past January, when he sat with Uncle Eddie in an Atlanta hotel the night before the NFC championship against the Falcons. DeBartolo gave the cuff links to York with a note that read, "It's your time to get what's yours."

As York speaks, holding the cuff links in his palm like dice, the pain he has spent years internalizing surfaces. His eyes dampen, and his mind drifts off. His office is both loud and quiet. Then he catches himself and puts the old gold back into the scarlet box.

INSIDE A BATON ROUGE bar, a man slid a piece of paper across the table into the hands of Eddie DeBartolo Jr. It was March 1997. For years, DeBartolo had been courting former Louisiana Gov. Edwin Edwards, a longtime friend of his father's, hoping that Edwards could help him secure a state gambling license to open a riverboat casino. But Edwards had demanded a price, and the price kept rising. He wanted Super Bowl tickets and part ownership in the casino, and then, at the bar, he reached into his pocket and passed DeBartolo a note with the final charge: "$400,000."

"This has to be taken care of by next week," Edwards said, "or there is going to be a serious problem with your license."

DeBartolo was scared, a rarity for a power broker so vain and combustible and generous. But Eddie and his sister, Denise DeBartolo York, had just begun to manage their deceased father's vast fortune of real estate, racetracks and the ultimate prize, the 49ers. DeBartolo had also launched his own real estate company, and he badly needed a successful development. His first project -- replacing the "pigsty" that he called Candlestick Park with a new$400 million stadium and an adjoining mall -- was off to a rocky start.

DeBartolo had spent years lobbying San Francisco politicians and unions and environmentalists to secure a ballot measure to allow public funds for a new stadium to be built next to the old one. The vote was three months away, and polls showed him losing. DeBartolo was campaigning around town at all hours, visiting bars and union halls. His desperation seemed to cloud his judgment. He'd already given Edwards Super Bowl tickets and caved on the ownership stake, and though his advisers had warned him to stop dealing with a crooked former politician, he panicked at the bar.

"I'll take care of it," DeBartolo said. One week later, he handed Edwards a briefcase full of crisp $100 bills, totaling $400,000. That decision has haunted the DeBartolo family and the 49ers franchise ever since.

THREE MONTHS LATER, in June 1997, Jed York, then a high school sophomore, woke up in his parents' Youngstown, Ohio, home to the news that his Uncle Eddie had won -- barely -- the measure for a new stadium. The oldest of Denise and John York's four kids, Jed didn't know much about stadiums, but he'd always been a favorite of both his grandfather and uncle. He had inherited some of their most defining traits: the elder Eddie's guts, the younger Eddie's temper. Uncle Eddie was his godfather, and they sort of look alike. Black hair, heavy eyebrows over warm eyes.

Jed always felt comfortable hanging with the big boys. At age 7, he would fly on his grandfather's private plane to 49ers games, playing gin with the adults on board, the hands sometimes eclipsing $1,000. Even from a young age, Jed always wondered, What can I do to carry on the family legacy?

By the end of 1997, that question took on new significance when DeBartolo's payoff came to light. Turns out the feds had been wiretapping Edwards for months. The former governor was convicted on 17 counts of racketeering, and DeBartolo was charged with fraud. He pleaded guilty to failing to report a bribe, paid a $1 million fine, ceded control of the 49ers to Denise and accepted a one-year suspension from the NFL. Any chance of a new stadium went down with him. "Louisiana killed it and hung it on a vine," says Carmen Policy, the former 49ers president.

But Louisiana did more than kill a stadium. It crushed the DeBartolo family and damaged the relationship between Eddie and Denise, igniting years of tension. It also changed Jed York's future in ways that as a teenager he couldn't have foreseen. In 2000 DeBartolo surprised everyone by declining to return to the 49ers following his suspension. There was just too much baggage. He and Denise divided the family assets: Eddie took the real estate holdings and relocated to Tampa; the Yorks got the 49ers.

The team was a train wreck, on and off the field. An iconic franchise had fallen from perennial Super Bowl contender to single-digit win totals, plagued by constant salary cap woes. The Yorks decided to start running the business prudently, an affront to Mr. D's tradition of lavishness. During home games at the eroding Candlestick Park, fans chanted "Fire the owner!" DeBartolo and John York traded barbs in the media. At one point, a few 49ers staffers removed some pictures of the former owner from the facility, whitewashing the past as dysfunction defined the present.

The only thing the two sides of the family agreed on was that the team desperately needed a new stadium. John York spent years trying to revive his brother-in-law's plan, but the area near Candlestick had neither the space nor the infrastructure for a new stadium and mall, and the city didn't have the money for fixes. In 2006 John York announced that the team was turning its attention to an empty lot in Santa Clara, 38 miles south of San Francisco. "We started over," he says.

The idea that the 49ers could leave the city infuriated fans. It also painted the owners into a corner: They had to make it work in Santa Clara, and they had to do so with little public support and no promises of public money; the construction costs would have to be privately financed as the U.S. economy was heading into the Great Recession. Still, John York cobbled together enough signatures and local support to get a ballot measure permitting the team to build a Santa Clara stadium, to be completed by 2015. The vote was scheduled for June 2010, and John York knew, as he says now, that to have a prayer of winning, the team needed "a fresh face."

So he handed the franchise over to his 29-year-old son.

"THERE'S NO TEMPLATE for this," Jed York says on an August morning, walking within the shell of the stadium.

Around him, 1,200 workers are busting their asses. York is wearing a hard hat and a yellow construction jacket over a black suit and scarlet tie. He talks about every nut and bolt of the stadium like a marketer would: energetic, polished, always on. He seems too young to be building a stadium, but he's been deeply involved in the franchise for almost 10 years. It's his team now. He's in control.

He reminded everyone of that recently when he stepped out in front of the situation regarding Aldon Smith, the star linebacker arrested for his second DUI in two years. Moments after a late-September loss to the Colts, Smith made a brief statement, apologizing and pledging to enter rehab. York then stood at Smith's locker to answer questions for him, taking the bullets so that Smith -- and coach Jim Harbaugh and GM Trent Baalke -- didn't have to. "I will take any shots that anybody wants to write about the organization," York told the media. "You can direct them to me, and I will support Aldon as long as he's willing to work at this and fight to get better." Players appreciate the little things York does, like attending the opening of Vernon Davis' art gallery and publicly backing Kyle Williams after his disastrous fumbles in the 2011 NFC title game.

York now realizes that he's spent his entire life preparing for this job. He graduated from Notre Dame -- just like his grandfather and uncle -- in 2003 and worked for two years in New York as a financial analyst. Then, in 2005, he shifted to the Niners and spent the next four years embedded in every facet of the organization. His parents gave him one responsibility: to learn, for York had known since his freshman year in college that one day he would take over.

Jim Harbaugh and Colin Kaepernick have failed to replicate their offensive success from 2012. Jonathan Ferrey/Getty Images

And that's precisely what many San Francisco fans were afraid of. When York did assume control in 2009, he was viewed not as a savior but as the latest in a series of trust-fund debacles. Jed somehow needed to cast himself as a break from the past, even as he relied on his family for guidance. "His role was to perform well," John York says. "We stayed in the background."

Really, Jed's role was to sell the new stadium. Facing stiff winds, he consulted one of the few people who could relate: Uncle Eddie. "Treat it like a campaign," he told his nephew. York took the advice and dusted off his uncle's playbook. He spoke with voters at restaurants, bars and coffee shops, just as DeBartolo had in the 1990s. In one bar in the Castro, a patron asked DeBartolo, "How do you feel about gays?"

"Eh, you know," DeBartolo said. "I feel fine about them."

"Would you give me a kiss?"

"Well, it depends where you want to be kissed. But I'll do anything for a vote!"

York went even further than his uncle had, going door to door in Santa Clara. Four nights a week for a year, he entered strangers' houses, sometimes bearing coffee and cookies, where voters waited, armed with questions. Most residents were concerned about one particular topic: traffic. But others asked about York's first major decision, hiring Mike Singletary as head coach, a move that looked worse after each 49ers loss. Still others would just try to get under his skin by saying: "Your parents don't know how to run a football team. You shouldn't run one either." One night, a voter got straight to the point, asking, "Are you really serious about building a stadium in Santa Clara?"

York replied: "I'm in your living room on a Friday night at 11 o'clock. I'm serious."

Some of his co-workers knew why he was so determined. York would say only vague things like, "My family didn't have a fun time from 1998 to 2000." But to those around him, the pain came through in brief flashes, his eyes glassing up when conversation turned to his parents or his uncle before he'd catch himself. They knew that he was really waging two campaigns -- one for the stadium, another for forgiveness -- and that in his mind they were intertwined.

York also has a personal goal: to get Uncle Eddie, who's won more Super Bowls than any other owner, inducted into the Pro Football Hall of Fame. The first step was to reintroduce him to fans. In 2009, at his first home game after taking over, York honored DeBartolo at halftime. It was the first time the 49ers had celebrated their former owner in more than a decade. Jerry Rice introduced him, and DeBartolo fought back tears as the crowd erupted, filled by a rush that had once sustained him. Then he returned to Tampa, back in the shadows, an exiled ghost, to advise from afar.

Meanwhile, York continued working coaches' hours, sleeping at the office. And his block-by-block canvassing gradually shifted public opinion. On June 8, 2010, ballot Measure J passed with 58.2 percent of the vote. York had the land. Now all he needed was a better football team.

And $1.3 billion.

IT WAS ALWAYS an exercise in faith, this stadium. Though the reality that it's being built has long settled in, when York stands at the highest deck -- the Green Roof, as they call it -- he still seems in awe of the simple fact that it exists. Dude, we built a stadium! He peers over the ledge to a mass of dirt that next year will be the field. "It's going to be the coolest area in sports," he says.

And not only because of the amenities. The team is pretty good too. Strange to think that only a few years ago the 49ers were, as York says, "the worst team in football." The losing under Singletary galled him. In Uncle Eddie's style, York would explode after losses, punching holes in walls. After the 49ers dropped the 2010 opener against the Seahawks, York stalked into the San Francisco locker room and pounded a chair against a wall until it broke. "I knew at that point that we didn't have the right coach," he says. "And I was very upset."

He consulted his uncle, who'd burned through three coaches before hiring Bill Walsh. "If it isn't working, make the decision," DeBartolo told him. York fired Singletary in December that year and began an overhaul of the team's structure. York had a long conversation with Bill Belichick, who along with Patriots owners Robert and Jonathan Kraft had become an informal mentor. Belichick told York that before hiring a coach, he should answer a simple question: "What kind of football do you want to watch?"

York wanted a quarterback-driven team and a quarterback whisperer as coach, owing not only to necessity in today's NFL but to 49ers history. But mostly, he wanted a smart franchise. So York promoted the team's salary cap manager and analytics specialist, Paraag Marathe, to COO. He handed the GM job to Baalke, an unknown 49ers personnel director whose judgment he implicitly trusted. York told Baalke that he didn't want to be one of those owners who pick players but that he needed to play a central role in finding the right coach.

Together, York and Baalke targeted Harbaugh, the Stanford coach who'd emerged as a favorite for jobs with the Dolphins, Broncos and the University of Michigan. The 49ers interviewed him first, for five hours. DeBartolo called Harbaugh on behalf of his nephew, just to remind him of what happened the last time the 49ers hired a coach from Stanford.

At the interview, York made a curious decision: Rather than refusing to let Harbaugh leave unsigned, he intentionally allowed him to leave unsigned. York knew that Harbaugh's wife, Sarah, had just given birth. "Give him some space," York insisted. That night, amid rumors that the Dolphins were sending a private plane for Harbaugh, York told his staff, "If it's meant to be, it's meant to be." The next morning, as York says now, "Jim chose us as much as we chose him."

One year later, Baalke would win executive of the year and Harbaugh would claim coach of the year as the 49ers reached the 2011 NFC title game. And they did it with Alex Smith, whom the team did not consider to be a franchise quarterback. The Niners brass had been grooming an unknown passer they thought could take the team even further. In the 2011 draft, Baalke and Harbaugh had traded up to pick No. 36 for Nevada's Colin Kaepernick -- a decision that was based in part on a proprietary study about college passers compiled by 49ers assistant coach Geep Chryst and Marathe. Many observers thought the mobile quarterback would go late in the second or early in the third. But he turned out to be more than a coup: He validated a belief system that dates all the way back to Walsh and Uncle Eddie.

The 49ers believe that draft picks are essentially coin flips, no matter the talent level of the players or the evaluators. So they simply play the odds by accumulating picks: The 49ers had an NFL-high 13 before this year's draft and will have 11 in 2014. The numbers allow Baalke to take risks, just as the 49ers did in the 1980s when they traded second- and fourth-round picks for Steve Young even though they already had a Hall of Fame quarterback in Joe Montana. So Baalke bundled the 45th, 108th and 141st selections to move up and snag Kaepernick, who as he says now "was the guy we wanted."

The 49ers were building something special, even if nobody except insiders could see it. York had sold the stadium to Santa Clara on faith. He had met with sponsors and season-ticket holders and completed the hundreds of tedious but crucial tasks for a new stadium by asking people to believe in him. Now York had to persuade one more crucial group of people to take a leap of faith with him: the bankers.

YORK KNEW THE money men would play hardball. He was sitting in a New York skyscraper in the summer of 2011, having finished a pitch to a major bank. Seated next to him was his new team president, Gideon Yu, then 40, the former CFO of Facebook and YouTube whom York had hired with a clear mission: Persuade banks to loan $1.3 billion to the franchise and an agency that would manage the stadium.

It was ballsy that York and Yu were even pitching banks in 2011. After joining the team, Yu -- tall and skinny, a fast talker and an even faster thinker -- had produced a stadium state-of-the-union report, detailing the reasons the project could meet York's 2015 deadline. Even with $200 million from the NFL in startup money, York had to raise nearly $1 billion over the next two years, more than twice what most owners borrow for new stadiums. But after he discussed with Yu the combination of low interest rates on loans, good projections on ticket sales and how Silicon Valley's young millionaires would buy expensive suites, he asked his team president, "Why can't we just do it now?"

By that, York meant accelerating the stadium opening to 2014. Yu felt it was a huge risk. To meet construction deadlines, they'd have to raise $850 million in about a month. Yu reminded York that banks usually entertain such requests only once, and they would need to see how the loan would be repaid. But the 49ers were still working on sponsorships and had yet to sell any seat licenses. And if they couldn't sell hundreds of millions of dollars' worth of those licenses, the family might have to sell the team -- or, per league rules, the NFL could seize it and sell it -- to repay the loan. "That would be the consequence of a bad decision," Yu says now.