Suddenly, a season that looked so promising three weeks ago now appears clouded with questions.
Playing with what seemed like a Seahawk hangover, the 49ers lost to the Indianapolis Colts at Candlestick Park Sunday afternoon, 27-7, to fall to 1-2.
It’s the first time in the Jim Harbaugh era the Niners have lost back-to-back regular-season games and the first time his San Francisco team has been under .500.
After being crushed in Seattle by the Seahawks last Sunday night on national television, the 49ers had a chance to get their confidence rolling again with a win over Indianapolis, but instead the 49ers were unable to play with any consistency.
Quarterback Colin Kaepernick had his second bad game in a row, completing just 13-of-27 throws for 150 yards – more than 50 of those yards coming after the game was decided -- lost a fumble that led to a late Indianapolis touchdown, threw a late interception and couldn’t get free as a runner on the read-option, which was bottled up by an active, quick-moving Colts defense. It was Kaepernick's first loss as a starter at Candlestick Park.
And defensively, the 49ers couldn’t stop the Colts on the ground or contain quarterback Andrew Luck, who completed 18-of-27 throws for 164 yards, ran for a touchdown and guided his team to two other touchdowns and two Adam Vinatierri field goals.
Also, the penalty problem – which was so pronounced during the loss at Seattle – again was an issue. With the game still on the line early in the fourth quarter, the Colts 11-play, 80-yard touchdown drive to go up 20-7 was aided by two flags on the 49ers secondary. San Francisco was penalized six times for 48 yards.
After the Colts took a 7-0 lead in the first quarter, the 49ers responded with Kendall Hunter’s 13-yard touchdown run to tie the game. But the 49ers then watched the Colts score 20 unanswered points.
Now, already two games behind the 3-0 Seahawks in the NFC West, the 49ers have just three days to prepare for a Thursday night game in St. Louis against the Rams, an important division game.
So, what’s happened to these Niners?
After the offense opened the season in dynamic fashion in a lopsided win over Green Bay, the 49ers have looked almost inept the past two weeks.
The tale of the tape Sunday against Indianapolis was in the Colts favor in turnovers (2-0), time of possession (36:25 to 23:35), first downs (23 to 14), total yards (336 to 254) and sacks (3 to 1).
Harbaugh now faces the biggest challenge of his career, trying to right his team’s ship while also dealing with off-the-field issues regarding Aldon Smith’s arrest (he may be headed for rehab), a groin injury to Patrick Willis and a hamstring injury to Vernon Davis that makes their status for the Rams game questionable and the fact opposing defensive backs the past two weeks have been able to bottle up his receiving corps (especially with Davis out of the lineup Sunday). A second viable wideout option behind Boldin has yet to emerge, and Quinton Patton – who looked so good in the preseason – has been forgotten.