SANTA CLARA -- Have the 49ers gone rogue?

The days of glittering Super Bowl trophies have given way to a new type of parade: allegations involving bomb threats, brass knuckles, automatic assault rifles, public intoxication and drunken driving.

In all, there have been nine arrests involving 49ers players since 2012. . That's the most in the NFL during that span, according to a review of NFL crime databases compiled by profootballtalk.com and utsandiego.com.

The legal troubles tarnish an organization otherwise soaring, with three straight NFC Championship game appearances and a sparkling new $1.3 billion stadium set to open this fall.

For those 49ers who remember better days, the rash of bad publicity does not sit well.

"They have to think about what Bill Walsh used to tell us: 'Be accountable off the field as well as on the field,'" said former running back Roger Craig, who was part of three Super Bowl champions in the 1980s. "I see their young guys making the same mistakes over and over. Somebody needs to get in their ear and talk to them."

Star linebacker Aldon Smith accounts for four of the 49ers' arrests, including April 13, when the All-Pro pass rusher allegedly became belligerent at Los Angeles International Airport and told a Transportation Security Administration officer that he was in possession of a bomb.

The arrest figures do not include star quarterback Colin Kaepernick or young receiver Quinton Patton, who are being investigated for a "suspicious incident" after a purported night of partying at a Miami hotel. No charges have been filed in the case, and coach Jim Harbaugh said Friday: "I've seen one side reported. I've heard the other side. I feel very good there'll be a good resolution, and hopefully a just one, too. I hate to see his reputation be the victim."

Asked about the recent run of negative headlines, general manager Trent Baalke said: "One (arrest) is too many, OK? We just have to do a better job. And that's the mentality of this group and that's the mentality of this ownership. To think that we don't care? I take offense to (words like) 'classless' or 'lawless,' because that's far from the truth.

"Because if you're in there every day, if you're in the locker room with the majority of those guys, those are damn good guys that work awfully hard. ... Respect the masses because the masses are doing it right, and we'll get the other things fixed."

The trouble might represent a mere blip on the police scanner. But it also might signal the new price of success. As the arrests mount, it's time to wonder if the 49ers' willingness to take on players with questionable backgrounds represents a shift toward an edgier, more volatile culture.

Other episodes have led to undesirable press clippings: rookie cornerback Chris Culliver made anti-gay comments during the Super Bowl media day in 2013 in New Orleans; Pro Bowl linebacker Ahmad Brooks hit a teammate over the head with a beer bottle last June outside his San Jose home; Culliver, who had been working hard to rehabilitate his image, was arrested in March on suspicion of hit-and-run against a bicyclist while driving on a suspended license and was found in possession of brass knuckles.

The 49ers' off-field developments have raised some eyebrows around the NFL. The Bay Area News Group interviewed more than 20 people, including former players, coaches, general managers and agents, who discussed the 49ers' arrests and the challenges of evaluating character in the social media age.

Second chances? Or a blind eye?

In the three years before Harbaugh and Baalke took charge, there were four arrests involving 49ers players. In the three years since, the arrest figure has more than doubled. All five of the players who have been arrested in that span remain on the team.

At least one opposing front-office man has a simple explanation for the spike: "It just seems like they're on a bad run," the executive said.

Still, the 49ers seem unafraid to bank on players with checkered pasts, as well as to show forgiveness for their missteps. As for the troubled linebacker Smith, Fox Sports 1 obtained a predraft psychological profile from a subscription-service scouting company that pegged the Missouri star as "a higher than average risk" for getting into trouble. Baalke confirmed Friday that the 49ers subscribe to that service and that they were aware of the red flag.

Under Harbaugh and Baalke, the team has acquired several players with at least one arrest on their resume: Alex Boone, Chris Cook, Perrish Cox, Braylon Edwards, Donte Whitner, Randy Moss and Eric Wright.

Wright, who was arrested for driving under the influence in 2012 while playing for the Detroit Lions, faced a DUI charge only days before the 49ers acquired him in 2013 in a trade from the Tampa Bay Buccaneers. (The Los Angeles County District Attorney's Office did not file charges in the latter case).

In some of those cases, notably Boone and Whitner, the players emerged as model citizens inside the 49ers locker room as well as major contributors on the field.

"It's a risk-reward business," Baalke said. "And we try to take chances -- calculated chances -- and it has worked in a lot of cases. There are other times when the character of an individual coming into the NFL was sterling. But they end up being guys who get in trouble.

"It's not always the guys that come into the league with a checkered past that leave the league with a checkered past. It can be the opposite. And if anybody in here has the answer about who is going to end up doing what, give it to me. I could use it."

Big talent, big concerns

No 49ers' trend is more troubling than the career path of Smith, the linebacker at risk of squandering his prodigious talent.

Smith has been arrested for DUI twice and turned himself in on felony weapons charges in June 2012 after a wild party at the four-story home he rented in the hills of East San Jose spun out of control.

Police arrived after receiving reports of gunshots to find two men shot and a third -- later identified as Smith -- suffering from a stab wound. Investigators' details later revealed that Smith and then-teammate Delanie Walker had both fired guns into the air in an attempt to get hundreds of partygoers, including alleged gang members, to leave.

Last September Smith was arrested on suspicion of driving under the influence after he was found passed out behind the wheel of a still-running car he had crashed into a tree. He is charged with having a blood-alcohol level of 0.15 -- nearly double the legal limit.

Some questioned management when the All-Pro pass rusher practiced with the team hours after he was released on bond. The scrutiny increased when less than 48 hours later, he played every snap of a 27-7 loss to the Indianapolis Colts.

After that Sept. 22 game, owner Jed York announced that Smith would be entering an inpatient facility for substance abuse. Smith, the team's sack leader, missed five games but returned for the team's third playoff run in as many years. He has never been suspended by the team.

Ronnie Lott, the legendary 49ers defensive back, has taken a personal interest in Smith's well-being, taking time to meet with the linebacker.

"I'm worried about him as an individual," Lott said after the LAX incident. "He's got so much ahead of him as a person -- forget about football -- as a person."

Smith has a hearing in Santa Clara County Superior Court on Tuesday.

The 49ers probably will wait for the courts and league to act before deciding his playing status for 2014. The NFL might suspend him and the 49ers could take disciplinary action, as well.

"We're a family," Baalke said. "You don't just open a door and toss people out of it. You continue to work -- until they leave you no choice."

Former Raiders quarterback Rich Gannon, a one-time league MVP, said the only reason that threshold hasn't already been met is because of Smith's extraordinary pass rushing ability.

"He'd probably be gone by now but he's a unique talent," said Gannon, who has met Smith. "He's probably a decent guy. But he's got some demons he's trying to fight through. And just because you're a decent guy doesn't mean you're a good decision-maker, and clearly he's made some really poor decisions that he has to be accountable for."

Judged on wins, losses

The 49ers are 36-11-1 since the off-field trouble began in earnest, with one Super Bowl appearance to go with those three NFC title games. Across the league, there is empathy for the 49ers' plight because even rival executives know what the job is all about.

"I don't think you can fault the 49ers for what they're doing because the real basis of this is what? It's wins and losses," said Ron Wolf, a former Green Bay Packers general manager. "That's how you're judged, and no one can do better than they've done."

Carmen Policy, a 49ers executive from 1983-1998 who helped create a sports dynasty in San Francisco, said societal changes make comparisons to the past almost moot.

The 24/7 news cycle, the lack of privacy in the social media age and an erosion of authority figures has contributed to the 49ers' situation.

"The authority of the coach isn't what it used to be," Policy said. "Nor is respecting the brand or shield. There is no bigger picture: just the image in the mirror."

Policy said the relative inexperience of York, at 32 the youngest NFL owner, has not complicated the 49ers' problems. He said the coach is responsible for team discipline, with executives acting in a supporting role.

"It's part of his authority and you don't want to overstep it, especially with a personality like Harbaugh, who seemingly had everything so put together the first couple of years," Policy said.

Gannon, who knows Harbaugh from his time as a Raiders assistant, said the coach and general manager take off-field behavior seriously.

"I think they think the same way when it comes to what type of player (they're looking for)," he said of Harbaugh and Baalke. "You want high-character individuals that do the right thing when no one's watching."

Gannon also recalled the perils of sharing a locker room with troubled players. He remains forever frustrated by "guys that were more concerned about having a good time than winning football games, guys that quite frankly put the entire team at risk because they got themselves in trouble and weren't able to play, disciplined, suspended," he said. "It gets to the point where it just wears you down."

Baalke said that the social media era throws another wrinkle into the character evaluation process. It's already tough to predict how fame and money might alter the personality of a young player transitioning from college to the NFL.

Now, they must envision how the prospect will handle round-the-clock scrutiny.

"It's made life for general managers even more difficult because it's nonstop," he said. "But this is what (players) signed up for, right? So they have to understand that significance of their actions as men. Not as players, as men. They have to understand that when they do something wrong, especially in the society that we live in now, that negativity sells."

Players' taking ownership

In one sense, the 49ers are no different from any team that is susceptible to their players' questionable off-field behavior. What is occurring in San Francisco is not an anomaly. Since Harbaugh and Baalke took over the 49ers, 153 players leaguewide have been arrested, including New England's Aaron Hernandez on murder charges.

But the NFL has received more scrutiny for other issues such as the handling of concussions and the bullying of former Stanford star Jonathan Martin in Miami.

"Some of these things these guys are getting involved in, it's just carelessness," former Raiders receiver Tim Brown said. "No respect for the position that they hold, or not enough respect."

Craig, who made four Pro Bowls during a 49ers career that lasted from 1983-90, said Walsh fostered a culture in which players were taught to act "as an extension of each other."

That didn't stop when players left the field. And while Walsh delivered the message, Craig said locker room leaders such as Jack "Hacksaw" Reynolds, Charle Young, Willie Harper and Ronnie Lott carried it through. He chuckled a bit while recalling the many times Lott, a fearsome safety, would summon the players to clear the air.

"Ronnie would call a meeting and it would be players-only," Craig said. "What we did as football players was to take ownership of the team and say: 'Stop this kind of stuff.' Ronnie Lott was like the CEO of our team. When he talked, we listened."

Now, Craig called on the team's current leaders to do the same. The 49ers' most respected veterans, such as linebacker Patrick Willis, running back Frank Gore and defensive end Justin Smith, aren't known for their speechmaking. But Craig said recent incidents should serve as "a wake-up call."

"I think the team could do it now," he said. "Patrick Willis. Vernon Davis. Kaepernick. They have some strong voices and they can pull those guys in to be on the same page."

Beyond veteran players, all NFL teams employ someone to oversee player engagement, essentially a round-the clock resource for players as they navigate the pitfalls of being young, rich and in the spotlight. But former player Troy Vincent, now the NFL's executive vice president of football operations, said players also must accept their role.

"The resources that are available to the players are unlimited," Vincent said. "The challenge is we can only assist those who are looking for it."

Policy said he does not hold management responsible for the 49ers' off-field incidents. But he added that team officials need to pay attention to who their players hang out with to help them make the transition to a professional culture.

They also need to foster a peer-to-peer policing in the locker room, Policy said.

"The less authority you have in your life the tougher it is to handle" the NFL, he said. "It's all coming to roost now."

Staff writers Steve Corkran and Cam Inman contributed to this report. Contact Daniel Brown at dbrown@mercurynews.com, Elliott Almond at ealmond@mercurynews.com and Jerry McDonald at jmcdonald@bayareanewsgroup.com.