SAN FRANCISCO -- The "jive turkey gobblers" talk has gone into hibernation, along with the too-hard handshake and "what's your deal?" instigation.

Jim Harbaugh just surrendered his license to be full-throttle Jim Harbaugh. For a while, he'll have to make do with being a good football coach, minus bully pulpit, Dr. Seuss vocabulary and smirking certitude. His map to a world where players might be "above reproach in everything," a fantasy island if ever there was one, disintegrated with the decision to make Sunday's game a pit stop on 23-year-old Aldon Smith's route to substance-abuse treatment. The game itself, a 27-7 Colts win, was San Francisco's second straight blowout loss, and the first time the 49ers have lost two in a row under Harbaugh. It left them at 1-2, making this the first time since the end of Stanford's 2008 season that a Harbaugh team has had a losing record.

That sort of success with two separate reclamation projects, plus a Super Bowl trip in his sophomore year as an NFL head coach, would make anyone prone to a sense of invincibility. Harbaugh's didn't require much cultivation. He loves to talk about "humble hearts" and the dangers of hubris, but he could give the Dodgers lessons on celebratory cannonballing into an opponent's pool.

After Sunday's loss, Harbaugh looked genuinely and thoroughly humbled. His eyes had the slightly glassy quality they often do at news conferences, as if he has a few dozen other things on his mind. But it was different this time. Usually, he tries to withhold answers. Now he seemed to be short on them, just as he had been a week earlier in Seattle, where the Seahawks turned his team into a gelatinous mess.

He broke from his pattern of delivering the most efficient responses possible when a reporter asked if, after two dreadful losses, he was confident the 49ers could find their way back.

"Yes," he said, almost leaving it at that. And then … "We have no choice. No choice but to find our way."

For the record, he did not sound confident. He barely sounded determined. If the interview had been conducted over the phone, no one would have believed the speaker was Jim Harbaugh.

At the moment, he may not recognize his team. The 49ers sit one spot from the bottom of the NFL rankings for penalties, averaging 9.7 per game. They averaged 6.6 last year. Against the Colts, two third-down incompletions by Andrew Luck became first downs via penalty.

The defense that carried the 49ers back to relevance in 2011 has not been outstanding since last November. The team that allowed a combined 10 rushing touchdowns over 32 regular-season games in 2011 and '12 has already given up six in three games. They have surrendered 351 rushing yards over their last two games, more than in any such stretch since 2004 … when they won only two games and earned the top pick in the 2005 draft … which yielded quarterback Alex Smith … who yielded his job last year to Colin Kaepernick … who is now 1-2 while, as many advanced math scholars are happy to point out, Smith is 3-0. They tend not to note that Smith's Chiefs have faced only teams that missed the 2012 playoffs, while all of the 49ers' opponents advanced last year.

That said, Kaepernick has delivered easily the worst performances of his brief NFL career over the last two weeks. He has thrown for a combined 277 yards and committed six turnovers after opening the season with 412 yards passing and zero turnovers against the Packers. The Colts' efforts to deny him open receivers was greatly abetted by the hamstring-induced absence of tight end Vernon Davis. This offense can thrive without the injured Michael Crabtree, Kaepernick's favorite target in 2012. But take away Davis, too, and the 49ers' passing game can make any defense look like vintage Steelers. Even when he doesn't touch the ball, Davis keeps defenders busy and loosens up the coverage elsewhere. Without him, Kaepernick attempted very few deep passes. He kept plying the sidelines, to little effect.

The one part of the 49ers' offense that seemed to work was the running game, yet they virtually gave up on it even as the score stayed within a touchdown. Frank Gore had 70 yards rushing on eight carries in the first half, and finished with 82 on 11 rushes.

There's a mother lode of second-guessing material on the stats sheet and game film, all of it fairly perishable. Good teams, even great ones, go through ugly stretches in the NFL. When they happen, they're incomprehensible. Then from a slight distance, these stretches begin to make sense, to become almost predictable ex post facto. They're much better endured in September than January. 

The decision to keep Aldon Smith in the lineup on Sunday -- less than 55 hours after San Jose police found his truck lodged against a tree and arrested him on suspicion of drunken driving -- will have more lingering effects. Even if the 49ers could produce a treatment counselor to validate CEO Jed York's contention that Smith benefited as a person from carrying on as usual, the choice would factor out as callous, blinkered and more than a little desperate. It seems the club couldn't look beyond Smith's pass-rushing brilliance, especially not with a quarterback of Luck's caliber coming to Candlestick, and think first of former Cowboy Josh Brent, now facing 20 years in prison for crashing his car while inebriated and killing teammate Jerry Brown Jr. They couldn't prioritize the memory of ex-49er Delanie Walker learning after the Super Bowl that his aunt and uncle had been killed by a drunken driver.

More than anything, they couldn't anticipate their next play, what would happen after Sunday, even with the help of scouting reports that show Smith had been arrested on similar charges in the past, been stabbed at a party in his home and been accused of firing a gun to scare away the worst of his guests.

After calling for Smith to be in Sunday's lineup, they effectively repudiated that choice at the last whistle. The next play turned out to be this: Smith apologizing to a crowd of reporters around his locker, with Harbaugh and GM Trent Baalke in the wings and York at his side, preparing to tell the media the young linebacker would be taking an indefinite leave of absence to tend to his personal problems. In politics, they call that a flip-flop. In football, it's bad coaching.

In his discussion with the media, York said the decision had belonged to Harbaugh and Baalke, though they discussed it with him. From the general public's perspective, the distinction must seem pretty minute. York will take heat, justifiably, for trying to cast the one-game prelude to the leave of absence as an accountability exercise that would help Smith. But in the locker room, the players could see this move for what it ultimately was: the judgment call of a coach who had restored the franchise, who had gilded every team he touched for the last 10 years. If he says something is right, it must be so.

But this call went bad from the start. Fans, in greater numbers than one might have expected, took to airwaves and online forums to express disapproval. Then Smith did not play all that well, a development that shouldn't have been surprising, especially if he took the field knowing he would be on an enforced sabbatical when the team plays in St. Louis on Thursday night.

"He hasn't been himself," safety Donte Whitner said. "Been a little quiet, like he feels like he let everyone down."

Asked whether he supported and understood the decision to put Smith in the game, Whitner paused and then said: "Uh, yeah, we've got to go with what Coach says. … Coach's call was to let him play, and he was out there and made some plays, so we'll see what's going to happen."

It wasn't a day of Harbaugh's "enthusiasm unknown to mankind." For the first time in almost two years, the 49ers and their coach have to confront doubt. Harbaugh is no longer Midas and Bo Schembechler sharing the same fleece sweatshirt. He's just a coach, and that must feel very strange.