The Takeaway: A New Low Under Harbaugh

Colin Kaepernick (Getty Images)

With Aldon Smith's arrest Friday, the 49ers find themselves in a state of flux going forward. Inside we break down what went wrong for San Francisco and where the team stands going forward with Smith's indefinite leave from the team. (Free Preview)

The San Francisco 49ers' record took more than one hit Sunday.

While the team suffered a difficult loss to a heavy underdog at home, it also backed itself into a corner with the handling of it's star outside linebacker after his recent arrest.

Just two days before Sunday's game, Aldon Smith was arrested on suspicion of DUI. Not only was he allowed to practice that day, but he was allowed to play in the game against the Colts.

"Our opinion is if you're sitting someone down and paying them to sit down when they're going to seek treatment in the future, we didn't feel like that was an appropriate punishment," 49ers CEO Jed York said Sunday.

"We're not trying to circumvent what the NFL will do. This is about making sure that Aldon has the opportunity to work on something, to get better, and he knows that he has our support and hopefully he has everybody's support in something that has been very difficult."

Smith will be away from the team indefinitely and likely get treatment for substance abuse in the meantime. His absence this week in St. Louis was the only thing made clear following the game.

York and the team allowed Smith, a star player with national name recognition, to play Sunday without a hitch. He started, played every snap and made five tackles.

But Smith clearly wasn't himself. The team clearly wasn't itself. For the first time since Jim Harbaugh took over as head coach, it lost back-to-back games. The resiliency that it became known for over the last two seasons was nowhere to be found against Indianapolis.

The 49ers played as though they were under a microscope. But it had nothing to do with football, like the microscope of a playoff game or Super Bowl.

The organization's integrity and morality were under siege in front of a national television audience. The players played like it. The coaches coached like it.

It was a shadow cast over the team before kickoff, because public perception wouldn't have found a win Sunday a good excuse to play Smith. A win with him in uniform would have felt like a defeat, because a football game would have been more important than right from wrong.

A loss with Smith suited up might feel worse.

Accountability, important in every circle, is always a topic players like to discuss when talking about trusting one another. In football, there's no trust without accountability.

The 49ers elected to forgo accountability by giving him their blessing to play.

Why, Jim Harbaugh, was Smith allowed to play?

"It was a decision we made," Harbaugh said.

York offered a more elongated answer.

"Our opinion was, sitting somebody down and paying them to sit down when they're going to seek treatment in the future, that didn't seem like an appropriate punishment. I know it might not sound reasonable, but for Aldon to be able to face the media, face his teammates, and take full responsibility for what he's doing, we felt that was the best situation for Aldon himself, and for the team, and ultimately for the community at large. And i realize people might not agree with that decision, but that was the decision that we felt was best."

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Between the lines, the 49ers simply could not make plays offensively when they needed to. The offense that prided itself on balance and explosive plays couldn't muster either in their 27-7 loss to the Colts.

It was a strange game. After throwing for 412 yards against the Packers and struggling to get the running game going, the 49ers completed just 48 percent of their passes and looked dominant on the ground.

San Francisco, a team that finished with the third-best running attack in the NFL in 2012, averaged 5.0 yards per carry, and lost by 20. The 49ers have been outscored 56-10 over their last eight quarters.

Since Harbaugh took over 2011, the 49ers have found ways to win without the passing game as long as they could run the ball. They ran the ball Sunday, but their insistence on balance did them in.

"Haven't been getting those drives, making those big plays," Frank Gore said. "Too many three-and-outs. We aren't getting in those types of rhythms."

Those rhythms have often been catalyzed by Vernon Davis, who is the offense's most complete player. He can be a huge asset in the running game with his blocking ability, and he's the team's most reliable down-field threat. His absence Sunday was more than palpable.

Anquan Boldin was the only viable threat in the passing game, making five catches on eight targets. The only other wideout to catch a pass was Kyle Williams, who had two for 12 yards.

"There wasn't enough opportunity to make plays," Harbaugh said. "The players not having the opportunity to make them and not making them.

Coming out of training camp, the obvious question would be how the team would deal with missing Michael Crabtree and Mario Manningham for at least the first third of the season.

That question appeared to be answered after Boldin's 208-yard performance in the first week of the season. But it's come up again once the offense was put on tape.

Davis' replacements, Vance McDonald and Garrett Celek, combined to make two catches on three targets. Celek's 30-yard reception didn't come until the game was well in hand late in the fourth quarter.

Neither Quinton Patton or Marlon Moore had a catch.

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