Floundering 49ers have big problems

Colin Kaepernick and the 49ers offense continue to struggle to move the ball. (AP Photo/Marcio Jose Sanchez

SAN FRANCISCO -- Pick a problem. There are plenty from which to choose.

That is what is so worrisome for the San Francisco 49ers as they are under .500 for the first time under coach Jim Harbaugh. Yes, the 49ers are 1-2 and trail rival Seattle (3-0) by two games in the NFC West. It is early.

Still, the 49ers have real problems. After a deflating 27-7 home loss to the Indianapolis Colts on Sunday, the 49ers are dealing with poor offensive play, mounting injuries and Aldon Smith's off-field issues.

The problems are serious and the beleaguered defending NFC champions -- who have been outscored by a combined 56-10 the past two Sundays -- somehow have to find a way to rebound on short notice. The 49ers play at the St. Louis Rams on Thursday. The Rams tied and beat the 49ers last season.

San Francisco will also go forward without Smith, their star pass-rusher.

A quiet locker room became a serious one Sunday afternoon when Smith made his first public statement since being arrested at 7:02 a.m. Friday on charges of drunk driving and possession of marijuana. Smith vowed to “fix” his problem. Then, 49ers CEO Jed York said Smith is leaving the team indefinitely to deal with a personal matter. Smith is expected to check into a treatment center this week.

Often, alcohol treatment plans are for 28 days. Thus, the 49ers may be without one for the most dynamic pass-rushers in the NFL for the next month. Smith, who turns 24 on Wednesday, deserves credit for trying to get a handle on his personal life. However, star athletes don’t often leave their teams in season to get treatment. Smith’s situation will be closely watched around the league.

The 49ers -- who were dominated at home by an Indianapolis team that was playing without six injured starters -- have several pressing, more traditional football problems.

It starts with the offense. It is amazing to think the unit on the field Sunday was the same one that beat Green Bay in Week 1. In that game, quarterback Colin Kaepernick threw for 412 yards and receiver Anquan Boldin had 13 catches. The 49ers were dynamic offensively.

They were anemic Sunday against a Colts’ defense that is not known as a giant killer. Kaepernick threw for 150 yards. Most of it was in garbage time. He had two completions at halftime.

According to ESPN Stats & Information, Kaepernick was 1-for-6 on passes that traveled more than 10 yards down field. Last season, Kaepernick completed 55.6 percent of such throws. It was the fifth best in the NFL. This year, he is completing just 37.8 percent.

Kaepernick went from being jaw-dropping good against Green Bay to totally ineffective the past two games.

It was not all on Kaepernick. His receivers could not get open for the second straight week after being shut down in Seattle. That poor performance was chalked up to the Seahawks’ superior secondary. That cannot be said about the Colts’ secondary.

The 49ers have to do something about getting their receivers open. Boldin is fine, but he needs help. Mario Manningham (knee) may be back in a month and Michael Crabtree (Achilles) is hopeful to return late in the season.

Perhaps it is time San Francisco returns to the read-option offense in which Kaepernick had success last year. The team has used it sparingly this season. Offensive coordinator Greg Roman said last week that could change.

With the offense desperate for a spark, there’s no doubt the 49ers’ coaching staff will consider everything.

It did not help that star tight end Vernon Davis was out with a hamstring injury. Sunday was his first missed game in six years. There is no guarantee he will be ready to face the Rams. Inside linebacker Patrick Willis -- the heart and soul of the team -- left in the third quarter with a groin injury. He declined to speak to reporters after the game.

As the 49ers try to figure what has gone wrong so quickly, they know their issues run deep. A hole has been dug. According to ESPN Stats & Information, since 1990 only 24 percent of the teams that started 1-2 made the playoffs.

“It is a pivotal time of the season,” safety Donte Whitner said. “But the sky is not falling. … We need to deal with this adversity.”