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  • Marcio Jose Sanchez / AP

    San Francisco 49ers quarterback Colin Kaepernick (7) throws a pass in the second half of an an NFL football game against the Indianapolis Colts in San Francisco, Sunday, Sept. 22, 2013. (AP Photo/ Marcio Jose Sanchez)

  • Josie Lepe / MCT

    49ers Colin Kaepernick (7) reacts near the end of the game as San Francisco falls to the Indianapolis Colts, 27-7, at Candlestick Park in San Francisco, California, on Sunday, September 22, 2013. (Josie Lepe/Bay Area News Group/MCT)

  • Paul Kitagaki Jr. / pkitagaki@sacbee.com

    San Francisco 49ers quarterback Colin Kaepernick (7) takes the field before the beginning of the game against the Indianapolis Colts in a game at Candlestick Park on Sunday September 22, 2013 in San Francisco, Calif.

  • Ailene Voisin

Ailene Voisin: From Kaepernick to defense, 49ers not making plays

Published: Monday, Sep. 23, 2013 - 12:00 am | Page 1C
Last Modified: Tuesday, Oct. 1, 2013 - 9:50 pm

SAN FRANCISCO – Is there such a thing as a GQ jinx? Growing pains? Too much, too soon? Excessive preseason hype and unreasonable expectations?

Whatever. But maybe. This little blip is transitioning into a supersized puzzle. The 49ers might not be in crisis, but the Super Bowl runners-up and their struggling young quarterback are nibbling at the edges.

Over the past two games, the offense has produced one touchdown and one field goal. The defense has been torched for 56 points. The combination has resulted in consecutive losses to the Seattle Seahawks (there) and Indianapolis Colts (here) and some surprising, serious head-scratching.

This is a first for Jim Harbaugh. His 49ers don't drop the ball two games in a row. They didn't do it when Alex Smith was here, and until Sunday's 27-7 humiliation handed down by Andrew Luck and the Colts, they didn't do it with second-year starter and projected superstar quarterback Colin Kaepernick.

So what gives? The mood swing certainly makes for a messy locker room. Within a matter of minutes late Sunday, the following occurred: Linebacker Aldon Smith apologized for his recent arrest on a DUI charge in a brisk, 41-second sound bite; club president Jed York attempted to justify why the organization allowed Smith to play against the Colts – not very convincingly, by the way – and then revealed the team's best pass rusher would be absent for an undetermined period of time; one 49er after another adhered to the company script, insisting Smith's arrest was neither a distraction nor a contributing factor to a stunningly subpar performance.

Then there was Kaepernick, seated alone in front of his locker, hands clasped, eyes staring at the floor, thoughts miles away.

"I'm frustrated with myself," he said, as usual, offering few details. "I have to be able to make throws down the field. They (Colts) put a spy (defender) on me, so I mean, they have one more to account for me. There's no one thing. We just didn't execute this offense."

Kaepernick, who was without tight end Vernon Davis (hamstring) and still missing wideout Michael Crabtree, was out of sorts from the opening drive. He looked nothing like the international celebrity who supplanted longtime starter Alex Smith last season after months of drama, led the 49ers to within a few feet of a Super Bowl victory, and a few months later, flexed for a bare-all cover of ESPN the Magazine.

Against a Colts defense that allowed 24 points to the Miami Dolphins at home last weekend, Kaepernick struggled to find his rhythm, his timing, his swagger, his touch. He missed long. He missed short. He missed badly. Kaepernick never found his footing, either. He completed 13 of 27 passes for 150 yards and ran for a meager 20. He also fumbled once, was sacked three times and was intercepted at the Colts' 3-yard line.

Furious with himself after his pass intended for Kyle Williams was deflected into the air, making for an easy grab for cornerback Cassius Vaughn, the normally composed Kaepernick barked an obscenity as he approached the sideline.

Whatever he was thinking, his were not pleasant thoughts. Cover boys are expected to be stars, to entertain, to win. Not happening lately, though. Sleepless in Seattle, and in San Francisco. His Seahawks contemporary, Russell Wilson, took control in the second half in Seattle. Luck, the former Stanford star who just happened to have played for Harbaugh, controlled the day at Candlestick and faked out everyone on a nifty 6-yard bootleg for a touchdown that essentially clinched the victory late in the fourth quarter.

"You can question just about everything right now," Harbaugh said. "We didn't play well enough to win in enough areas, on enough downs. We didn't make the plays. There wasn't enough opportunity to make plays. It was a combination of that, the players not having the opportunity to make them, and not making them."

It wasn't just Kaepernick, either. The 49ers were tagged for six penalties, with three assessed to Tarell Brown, and two infractions occurring on consecutive plays on a potential go-ahead drive.

The defense allowed 179 rushing yards, most of it in the second half. Harbaugh also has to be asking himself why he went away from Frank Gore after the running back rushed for 70 of his 82 yards in the first half.

The short week thus looms as a particularly interesting one. No Aldon Smith. Perhaps no Patrick Willis or Davis. A slumping young quarterback. Still no Crabtree.

"We all got to look at how we can (make plays)," Harbaugh said. "We gotta be real. We all have to look at ourselves to find out where we can get better."

Call The Bee's Ailene Voisin, (916) 321-1208. Follow her on Twitter @ailene_voisin.

© Copyright The Sacramento Bee. All rights reserved.

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