Are the San Francisco 49ers Being Beaten at Their Own Game?

Tyson Langland@TysonNFLNFC West Lead WriterSeptember 23, 2013

Sep 22, 2013; San Francisco, CA, USA; San Francisco 49ers head coach Jim Harbaugh stands on the sideline during action against the Indianapolis Colts in the fourth quarter at Candlestick Park. The Colts defeated the 49ers 27-7. Mandatory Credit: Cary Edmondson-USA TODAY Sports
Cary Edmondson-USA TODAY Sports

Coming into Week 3, head coach Jim Harbaugh had never suffered back-to-back defeats since taking over the San Francisco 49ers in 2011. Unfortunately for Harbaugh, his impressive streak came to an end on Sunday against the Indianapolis Colts

In surprising fashion, offensive coordinator Pep Hamilton’s offense and defensive coordinator Greg Manusky’s defense beat the 49ers at their own game.

The Colts’ ground game cranked out 179 rushing yards on 39 carries while securing nine first downs. Additionally, the Colts offense possessed the ball for 36 minutes and 25 seconds, whereas the Niners were on offense for 23:35.

Ahead of Sunday’s game, few believed Indianapolis would lean heavily on its rushing attack to take down the reigning NFC West champs.

Pundits have grown to trust quarterback Andrew Luck and Hamilton’s aerial assault, but they hadn’t seen enough prior to today to believe in Ahmad Bradshaw and Co.

Despite trading for first-round running back Trent Richardson this past Wednesday, the Colts fed Bradshaw early and often. The seventh-year veteran out of Marshall put together his best game of the season. He averaged five yards a pop on 19 attempts and scored his second touchdown of the season in the fourth quarter.

Through three games, the 49ers have allowed six rushing touchdowns. From 2011 to 2012, defensive coordinator Vic Fangio’s defense surrendered 10 rushing touchdowns. It’s safe to say his unit has experienced an early-season slump.

But what has caused the slump?

Aside from Aldon and Justin Smith, San Francisco’s front seven has looked average at best.

Furthermore, injuries and missed tackles have plagued this team. According to Pro Football Focus (subscription required), the 49ers are averaging 8.3 missed tackles a game.

To put that into perspective, the Niners averaged 4.1 missed tackles per contest in 2012 and 3.8 in 2011. Fundamental errors rarely happen to one of the best defenses in the NFL, yet Harbaugh’s club hasn’t found a way to right its wrongs with its back up against the wall.

Is Fangio’s defense starting to show its age, or is it premature to write off one of the league’s most heralded crews?

To err on the side of caution would be the correct move. Let’s not forget, San Francisco has had to shuffle personnel groupings due in large part to Ian Williams’ broken ankle and Patrick Willis’ groin injury.

Willis is easily the most important piece to the 49ers defense. Matt Maiocco of noted that Willis isn't likely to be available for Thursday’s game against the St. Louis Rams.

In addition, All-Pro outside linebacker Aldon Smith will probably miss the team's Thursday Night Football game.

Maiocco reported that Smith would take an indefinite leave from the squad and undergo treatment for substance abuse. Based on Smith’s past and his most recent episode, the organization is making sure he doesn’t let his problem endanger his future.

Offensively, this team is in the same state of sad affairs as the defense.

For the second time in as many games, Coach Harbaugh acknowledged his offense struggled to make plays. Here’s what the animated leader of men told reporters after the game, via Maiocco:

We didn’t make plays. There wasn’t enough opportunities to make plays. It was a combination of...the players not having the opportunity to make them and not making them.

He was right. Every time the 49ers had a chance to keep a drive alive, their receivers either let quarterback Colin Kaepernick down or failed to garner enough yards on third down. The Niners finished the game 3-of-12 on third down and only made one appearance in the red zone. 

Over the course of the last two games, San Francisco is 6-of-24 on third down and 1-of-3 in the red zone.

What gives? Well, the run game has been missing in action a majority of the time, and Kaepernick’s receivers haven’t done him any favors.

However, Kap hasn’t played well enough to elevate the play of his wideouts either. Without question, he has experienced the worst two-game stretch of his career. He’s not doing an efficient job of protecting the ball and not accurately finding his receivers downfield.

The loss of Pro Bowl tight end Vernon Davis didn’t make things any easier Sunday.

When Kyle Williams, Marlon Moore and Quinton Patton become your most serious threats in the passing game outside of Anquan Boldin, it’s safe to say it’s going to be a long day.

The 49ers have been beaten at their own game over the last two weeks, but that doesn’t mean this pattern will continue. Under Harbaugh, San Francisco has established itself as one of the NFL's most consistent teams on a weekly basis.

Will change take place overnight? That remains to be seen.

Nevertheless, we do know things will undoubtedly look better as soon as players start to get healthy. Moreover, this offense has to stop fooling around and start pounding the rock and controlling the clock.

The offensive game plan was centered on the ground game early on, but it abandoned the run in the second half. The 49ers need to get back to the basics so they can rely on running backs Frank Gore and Kendall Hunter.

The sooner Gore and Hunter start to shoulder the load, the sooner the Niners get back to beating their opponents instead of themselves.