Week 3 Rewind: 49ers lose to Colts, and their 2012 MVP
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Programming note: Watch today's 49ers press conference with head coach Jim Harbaugh streaming LIVE today at noon online here. 

What you need to know: The 49ers lost back-to-back games for the first time since Jim Harbaugh took over as head coach in 2011.

But that’s not even the worst part.

The team MVP from their Super Bowl run of last season, outside linebacker Aldon Smith, is expected to miss multiple games, beginning Thursday against the St. Louis Rams, as he enters in-patient treatment for substance abuse.

All-Pro inside linebacker Patrick Willis is out indefinitely with a groin injury.

And the 49ers’ 27-7 loss to the Indianapolis Colts on Sunday dropped the 49ers to 1-2 – the first time Harbaugh has been under .500 as an NFL coach.

[RELATED: Kaepernick, 49ers' offense struggle again]

Moreover, the 56-10 margin of defeat in the past two games, including the 49ers’ 29-3 loss to the Seattle Seahawks on Sept. 15, represents the team’s worst two-game stretch since they lost to San Diego (48-19) and Chicago (41-10) in back-to-back games in 2006.

Whether it's off the field or on the field, the 49ers are reeling.

Smith, the team's sack leader, was arrested on Friday at 7 a.m. on suspicion of driving under the influence and possession of marijuana. He missed the team meeting on Friday but took part in the practice later that day after posting $5,250 in bond. Harbaugh emphasized to his players on Friday to keep their focus despite the distraction.

Said Harbaugh, “I thought our team was ready to play. I thought our team was ready to play 100 percent.”

And Smith not only started, he played all 72 snaps in the game. He recorded five tackles. Afterward, Smith addressed the media as he read a statement:

“First off, I wanted to apologize to the team, the organization, my family and everybody I let down,” Smith said. “I also wanted to let it be known that this is a problem and it’s something that I will get fixed, and that I’ll do everything in my power to make sure that this never happens again.”

[RELATED: Instant Replay: A first under Harbaugh -- 49ers lose two in a row]

Team CEO Jed York said Harbaugh and general manager Trent Baalke decided to allow Smith to play on Sunday.

“It was something that was very disappointing to the team, and I think in talking with Aldon and knowing what he wants to do, there’s not a one-day fix,” York said. “This is a long-term fix. We support Aldon if Aldon is willing to fight for himself and try to make this right. And I will stand here and I will support him and I’ll take any shots that anybody wants to direct at the organization. You can direct them at me.”

The 49ers could not have suspended Smith without pay for Sunday’s game, but they could have deactivated him like they did a year ago when defensive lineman Demarcus Dobbs was arrested for suspicion of DUI and possession of marijuana on a Friday morning before a Sunday game.

“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,” York said. “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 the community at large.”

Head-scratcher: Running back Frank Gore exhibited a return to form on Sunday, as he averaged 7.5 yards per rushing attempt. The problem was he only carried 11 times for 82 yards. Gore rushed the ball three times in a four-play sequence and picked up 22, 11 and 21 yards on the 49ers’ only touchdown drive of the game. Kendall Hunter scored the only touchdown on a 13-yard run on a delay handoff.

In the second half, the 49ers had 15 offensive plays while they trailed by less than a touchdown. Gore carried on three of the 49ers’ first four plays of the second half for 12 yards. He did not get a handoff the rest of the game.

“I think the game kind of got different in the second half and we had to do what we had to do -- just throw the ball,” Gore said. “And that’s what it was.”

In the first half, the 49ers used three variations of a toss-sweep to Hunter and, even, No. 3 running back Anthony Dixon that netted minus-2 yards rushing.

Second-year running back LaMichael James was among the 49ers’ inactive players. He sustained a knee sprain in the 49ers’ final exhibition game. After the game, he suggested on Twitter he was a healthy scratch, writing “my knee feels fine” and “I'm ready to play.”

Lasting impact: The 49ers were down 13-7 late in the third quarter, and the Colts were backed up with a third-and-9 situation from their own 9. But 49ers cornerback Carlos Rogers got turned around in zone coverage and Reggie Wayne caught a pass, turned up field past Rogers and gained 25 yards.

On the play, pursuing linebacker Patrick Willis got his hands on Wayne and spun around awkwardly. He sustained a groin injury and could not continue. Willis appears doubtful to be ready to play against the Rams on Sunday. He declined comment after the game.

[RELATED: Willis' groin injury expected to keep him out]

Not threatening: Quarterback Colin Kaepernick has experienced the two worst statistical games of his 13-start NFL career in back-to-back games. After being responsible for four turnovers against the Seahawks, Kaepernick had a two-turnover outing against the Colts.

Indianapolis quarterback Andrew Luck threw for more yards than the dual-threat Kaepernick and he rushed for more yards, too. Kaepernick completed just 13 of 27 pass attempts for 150 yards with no touchdowns and one interception. His passer rating was 49.9. Kaepernick was sacked three times and rushed seven times for just 20 yards.

Said Colts coach Chuck Pagano, “The guy is scrambling around and our guys did a great job of containing him.”

“I have to play better,” Kaepernick said, later adding, “I’m frustrated with myself.”

Tight end Vernon Davis was inactive due to a left hamstring strain, and his absence was sorely missed. Wide receiver Anquan Boldin provided the 49ers with their only threat in the passing game. Boldin caught five passes for 67 yards.

Kyle Williams saw six passes thrown his way. He caught two for 12 yards. Marlon Moore, Quinton Patton and Kassim Osgood did not catch a pass.

Jon Baldwin, the first-round draft pick in 2011 whom the 49ers acquired in a trade for A.J. Jenkins, did not suit up for the game. Instead, the 49ers activated backup fullback Owen Marecic, who did not play.

Moving on up: Gore was the 49ers’ second-leading receiver with two catches for 21 yards. Gore now has 2,687 career receiving yards and moved past Hugh McElhenny and into second place on the franchise’s all-time list among running backs. Roger Craig holds the franchise record among running backs with 4,442 receiving yards.

Other injury concerns: Kyle Williams underwent X-rays on his left ribs after the game. He sustained the injury while throwing a backside cut block against Colts safety Delano Howell. Williams remained in the game.

Third cornerback Nnamdi Asomugha appeared to injure his right leg while pulling down Ahmad Bradshaw at the end of a 27-yard run in the fourth quarter.

Special-teams player Bubba Ventrone sustained a concussion while blocking on a first-quarter punt return. He did not return.

Defensive penalties: The 49ers were called for five defensive penalties that provided the Colts with first downs. Donte Whitner and Tarell Brown were flagged on the first two plays of the game.

Whitner was dealt an unnecessary roughness penalty for what referee Terry McAulay described as “illegal contact with the crown of the helmet by the defender.” In fact, Whitner hit Bradshaw with his right shoulder, replays showed, and it was Bradshaw who used the crown of his helmet to strike Whitner.

"It was a bad call," Whitner said. "I guess it was a big hit. Any big hit now in the National Football League is automatically a flag.”

Brown was called for three penalties. And three of the 49ers’ defensive penalties came on third downs and kept drives alive.

“Yeah, it was a rough day,” Brown said. “I think nine out of 10 times I would have got those calls or they would have gone my way. But I guess the referee saw something different. It happens. I’m going to play aggressive. I’m not going to change my style of play.”

[RELATED: Smith will seek treatment for substance abuse, miss Rams game]

Play time: The entire offensive line – Joe Staley, Alex Boone, Anthony Davis, Mike Iupati and Jonathan Goodwin -- and Kaepernick played all 53 snaps. The rest: Boldin 49, tight end Vance McDonald 47, Williams 44, Gore 42, Moore 22, Bruce Miller and Garrett Celek 21, Hunter 10, Patton 6, and Dixon, Osgood and Adam Snyder each played one snap.

On defense, Aldon Smith, Ahmad Brooks, NaVorro Bowman and Whitner played all 72 snaps. The rest: Brown 71, Eric Reid and Carlos Rogers 70 apiece, Justin Smith 57, Ray McDonald 56, Willis 48, Asomugha 38, Glenn Dorsey 34, Michael Wilhoite 24, Tony Jerod-Eddie 18, Demarcus Dobbs 16, and C.J. Spillman and Perrish Cox played one snap each.

Quote of the day: ”You can question just about everything right now. We didn’t play well enogh to win in enough areas on enough downs. Did not win the down enough. Not even close. They did. They made the plays offensively, defensively, and we did not.”
--49ers coach Jim Harbaugh

Looking Ahead: The 49ers (1-2) have a short turnaround with a Thursday night game at the St. Louis Rams (1-2). The Rams are coming off a 31-7 loss at the Dallas Cowboys. The Rams played the 49ers tough last season with a tie and a victory in two overtime games against the 49ers.