Chip Kelly, 49ers going through reboots -- together

Is Gabbert a better fit for 49ers than Kaepernick? (1:02)

Damien Woody and Jim Trotter both agree that Blaine Gabbert is a better fit in Chip Kelly's offense than Colin Kaepernick. (1:02)

SANTA CLARA, Calif. -- Your computer crashes. You reboot it. A couple of different things can happen.

The machine could spring back to life, like nothing was ever wrong, and appear to function properly. In your memory, there exists a problem, and you know that problem could come back at any time. But the way things look on reboot makes it tough to worry too much about it right now. For the purposes of this story, we will call this "The Chip Kelly."

Or it could take forever to fire back up, force you to shut it down and try again a few times, after which things just don't seem to work the way they used to work. It still looks like your computer, but you're not getting out of it what you used to get. For our purposes, we're calling this outcome "The San Francisco 49ers."

As the 2016 NFL season dawns, Kelly and the 49ers are pressing the reset button together. Which outcome should they expect?

"At Oregon, everybody bought into the system and what Coach Kelly was trying to do," said 49ers rookie defensive lineman DeForest Buckner, who played for Kelly as a freshman with the Ducks. "And I believe -- he couldn't really do it in Philly -- but if he gets all of the guys here to buy into his system, it'll be successful. Because I've seen it with my own eyes."

That's the hope, of course -- that what happened to Kelly in his truncated tenure as the Philadelphia Eagles' coach was the aberration, and that the success he had in college can translate to the NFL in his second professional stop. But the past three years have hollowed out the expectations for both Kelly and his new team. And as they start again fresh, it's more realistic to expect the slow reboot than the instant one.

Three years ago, Kelly and the 49ers stood on separate NFL pinnacles. Kelly was the red-hot college coach coming into the league with new ideas that would revolutionize the game. The 49ers were defending NFC champs who'd come within a few filaments of beating the Ravens in Super Bowl XLVII. The future looked blinding for both, and both made the playoffs that year.

But things deteriorated quickly after that. Kelly was unemployed before 2015's final game, and that 49ers team that was so recently one of the best in the league fell apart. Gone from those days are the likes of Justin Smith, Aldon Smith, Patrick Willis, Frank Gore, Anquan Boldin and Vernon Davis. A rash of retirements and other issues gutted one of the league's best teams in a stunning hurry.

"It was just a shock," said Niners linebacker NaVorro Bowman, one of the few 2013 stars who's still around. "At 28 and just having the guys that I played with for so many years, and the type of football that we played, and then throwing in guys that never played at that level of football, that was a challenge last year. Just to lose it so quick, that was a shock to everybody."

This was no one's plan -- Kelly and the 49ers together in 2016. Kelly was supposed to still be riding high with the Eagles, and Jim Harbaugh was supposed to be managing a 49ers dynasty in San Francisco. But here they are, together, hoping they can restore each other to the heights they occupied not long ago. Is that hope realistic? Can these 49ers really expect to contend?

"It all depends how fast we grow up," 49ers general manager Trent Baalke said.

That's a sobering assessment from a team official in a league where everyone's supposed to believe they have a chance every year. But what has gone on in San Francisco the past few seasons has everyone understandably realistic. Clearly, Kelly's time in Philadelphia showed he's no miracle worker, but the Niners are setting expectations a bit lower than that. After the tumultuous end of the Harbaugh era and the unfortunate entirety of the Jim Tomsula era, they're looking for something stable.

"He's the same guy every day," Baalke said of Kelly. "He's very concise in his communication with the players. They know exactly what he's looking for. He's demanding without being demanding, if that makes sense. I can't talk about what happened in Philly, but from my standpoint, communication has been natural and easy."

Kelly will have to keep it that way, and also bring some patience. This is a 49ers roster with major issues. There are questions to be answered on the offensive line and about second-year running back Carlos Hyde. Kelly's success his first year in Philadelphia was built around a healthy, excellent line and a league-leading run game. If he can't replicate that in San Francisco, it might not matter whether Blaine Gabbert or Colin Kaepernick is the quarterback. Kelly's offensive system relies on the run game above all else, and until that's established, there won't be a foundation. And until there's a foundation, nothing can be built. The 49ers know this.

"If people's expectations are still set on what we did with those guys, it's kind of hard to explain," Bowman said. "But there are some true fans, I think, that know you're willing to work and will take some punches with you. They know a guy like me is here, understands what they want I'm trying my best to get us there. It comes in time. It comes with the work that we're trying to put in now. And we'll get back to it."

And no, it might not be this year. The 49ers play in the same division as two of the best teams in the entire league. They're still putting back together a crumbled roster. They need Kelly to be a builder, and they need everyone to understand that building can be a slow process.

"Coach Kelly is the same person I've known since my freshman year," Buckner said. "I came here, people were talking about him being different. I thought I would see something a little different. But Coach Kelly's the same to me. Same guy."

Buckner says that as if it's a good thing. Eagles fans might hear it differently. Kelly's sameness might be just what the Niners need, or it might represent a stubbornness that keeps him from ever attaining the NFL greatness so many predicted for him.

The question is how much time Kelly gets to turn things around in San Francisco. Barring a hyper-accelerated meltdown of front-office relationships, he's sure to get more time than Tomsula did. Which means time to find a franchise quarterback -- especially if the 49ers have a crummy year and get a high draft pick.

For now, Kelly's staying out of the personnel decisions and focusing on trying to mold guys like Buckner, Hyde and Arik Armstead into franchise cornerstones. Basically, he and the 49ers are trying to restart in "safe mode." But maybe they end up with the best possible outcome for computer problems -- an entirely new machine.