SANTA CLARA -- Jim Harbaugh's band of merry mighty men was missing a few members at the start of this mandatory minicamp Tuesday.

Everybody wasn't on the same page, apparently. The big 49ers bandwagon had some notable no-shows.

And right now, for the first time in the Harbaugh Era, maybe a few 49ers folks are wondering if somebody out there really does have it better than them.

The facts: Tight end Vernon Davis and guard Alex Boone skipped Tuesday's minicamp opener to protest their current contracts, and cornerback Eric Wright surprisingly decided to retire.

These aren't unique events in the NFL or sports, but for this franchise, under this coach, it's a new wrinkle and sets a little bit of a different tone in 49ersland.

San Francisco 49ers’ Vernon Davis (85) threads the needle between three Baltimore Ravens defenders during the first quarter of Super Bowl XLVII,
San Francisco 49ers' Vernon Davis (85) threads the needle between three Baltimore Ravens defenders during the first quarter of Super Bowl XLVII, Sunday, Feb. 3, 2013, at the Superdome in New Orleans. (Nhat V. Meyer/Bay Area News Group) ( NHAT V. MEYER )

And yes, Camp Counselor Harbaugh noticed it and sounded just as frustrated as you would expect.

"I'm disappointed in that decision, for them not to be here," Harbaugh said of the absences by Davis and Boone.

"Not the decision that I envision being the 49er Way. Really nothing more to be said about it than: The focus will be on what's going on here."

Of course, it is only a June minicamp, and of course dozens of other talented 49ers players showed up to do the work and follow Harbaugh's orders.

The 49ers are still very good, and whatever happens with Davis and Boone, this team will be a Super Bowl contender in 2014.

Anyway, it's likely that Davis and Boone both will be back in camp before the start of the regular season, whether or not the 49ers make any financial concessions to either.


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"We'll address it," Harbaugh said. "And it'll come to a resolution. That's the deal that it is."

However, the 49ers just haven't experienced anything like this since Harbaugh and general manager Trent Baalke began the franchise's revival in 2011.

The 49ers have won games, worked in the trenches together, acquired talent, reached financial agreements quickly . . . and embraced Harbaugh's ideal of "the team" taking precedence over all individual rewards.

San Francisco 49ers’ starting quarterback Colin Kaepernick (7) is congratulated by San Francisco 49ers’ Alex Boone (75) after
San Francisco 49ers' starting quarterback Colin Kaepernick (7) is congratulated by San Francisco 49ers' Alex Boone (75) after Kaepernick's touchdown run against the Atlanta Falcons in the fourth quarter at Candlestick Park in San Francisco, Calif. on Monday, Dec. 23, 2013. (Nhat V. Meyer/Bay Area News Group) ( Nhat V. Meyer )

There have been little moments of discord here or there, but those were always doused quickly, or the offenders sent away in a blink.

The Harbaugh/Baalke 49ers have never gone through something like this -- two foundation players intentionally missing mandatory practice time while they are both under contract for two more years.

"Yeah, I think this is the first time," fullback Bruce Miller said of the unique experience of watching two teammates hold out in the Harbaugh era.

"Hopefully they get it figured out, get it settled and can come join us."

Once again, it's unlikely that Davis and Boone will continue their walkouts into the regular season; that would just cost them too much money.

For now, they can skip the offseason work and make their points while their fines are limited.

But it's also probably just as likely that 49ers management will refuse to give in to the holdout challenge. If Davis and Boone come back, they almost certainly will come back mostly on the 49ers' terms, not their own.

That's the 49ers Management Way, if I can paraphrase Harbaugh.

This is just all part of a larger 49ers picture, of pent-up financial pressure and the general understanding that this talented roster is about to undergo a very large salary squeeze.

Some of the 49ers' best players are reaching a certain age -- Patrick Willis is 29, Davis 30, Frank Gore 31, Anquan Boldin 33 and Justin Smith 34.

Some or all of their established starters have younger players being groomed to place them.

All of the current 49ers mainstays have watched some of their friends discarded -- Dashon Goldson, Donte Whitner, Jonathan Goodwin, Delanie Walker -- and replaced by younger, cheaper players.

Some of their established starters have accepted a little less than market value in order to stay with the 49ers.

And now . . . quarterback Colin Kaepernick -- with one year left on his old deal, it's important to note -- has just landed a deal that could end up paying him $19 million a season through 2020.

That's money that Davis and Boone (and Michael Crabtree and Mike Iupati) will never see; now that the 49ers have committed so much to Kaepernick, they have a lot less to give to everybody else.

All of which almost certainly has everybody in that locker room thinking, wondering and maybe even worrying a little.

Which leads to holdouts and some splintering of "the 49ers Way," or at least the way it used to be.

Read Tim Kawakami's Talking Points blog at blogs.mercurynews.com/kawakami. Contact him at tkawakami@mercurynews.com.

INSIDE

Vernon Davis, Alex Boone are no-shows. Eric Wright retires. PAGE 3