SAN FRANCISCO Two-game losing streaks are never good, but the 49ers' current skid seems particularly dark.
After losing 27-7 to the Colts on Sunday, the 49ers revealed that outside linebacker Aldon Smith, who crashed his vehicle in a San Jose front yard two days earlier, would miss the next game while he seeks help for a substance abuse issue.
They played without tight end Vernon Davis and finished the game without linebacker Patrick Willis and cornerback Nnamdi Asomugha, both of whom were hurt in the second half and are in danger of missing the next game.
Quarterback Colin Kaepernick had a second straight abysmal performance, the offense scored in single digits for the second consecutive game, and coach Jim Harbaugh has lost two contests in a row for the first time in his tenure.
To top it off, the 49ers (1-2) must travel to play the one division opponent St. Louis they could not beat last season, and they have a short week to prepare.
"We have no choice. No choice but to find our way," said Harbaugh, who was short on answers for why his team faltered.
A few minutes later, Harbaugh, general manager Trent Baalke and owner Jed York stood next to Smith, 23, as he admitted he had a "problem."
"It's something I will get fixed," Smith said. "I'll do everything in my power to make sure this never happens again. I also want to let everybody know that, once again, I'm sorry. Like I said, this won't happen again."
York then spoke, confirming that Smith, an All-Pro with 19 1/2 sacks last season, will miss Thursday's game against the Rams. He said Smith's leave of absence would be indefinite.
Smith played nearly every defensive snap against the Colts, and he finished with five tackles, including one for a loss. Asked why Smith played Sunday if he was intent on rehab, York said benching him didn't make sense.
"Sitting someone 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 team 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."
Smith was found in a stupor in the front seat of his pickup early Friday, his foot still pressing the accelerator. He was arrested for DUI and marijuana possession. It was his second DUI arrest in the last year and a half. Because of that, the NFL is likely to suspend him at some point, perhaps next season when the case has been adjudicated.
"We're not worried about that," York said of the suspension. "We're not trying to circumvent what the NFL will do. This is about making sure Aldon has the opportunity to work on something, get better."
For the second straight game, the 49ers were close at halftime but deteriorated in the third and fourth quarters. Penalties kept Colts drives alive and bad tackling a problem during a Week 1 win against the Packers was an issue again.
Late in the third quarter, the defense had the Colts (2-1) pinned at their own 9-yard line facing third and 9. Andrew Luck threw a two-yard pass to receiver Reggie Wayne, who weaved through tackles and broke others on his way to a 25-yard gain.
Willis was one of the defenders left sprawled in Wayne's wake, and he had to be helped off the field with a groin injury. With a short week to recover, Willis' availability Thursday is uncertain.
A week after Seattle's Marshawn Lynch had 98 rushing yards, the 49ers gave up 95 yards and a touchdown to Indianapolis' Ahmad Bradshaw.
"Felt flat, looked flat," cornerback Tarell Brown said of the defensive effort. "We all have to come out with a lot more intensity and start fast.
"We haven't started fast all year, and we're used to starting fast."
In 2011 no team could run against the 49ers, who didn't allow a rushing touchdown by Lynch until Week 16. Through three weeks this season, they have allowed six rushing touchdowns, three by the Colts.
"Stunned," safety Donte Whitner said. "We didn't play 49ers defense, and we'll go back to the drawing board. And we'll get it all corrected, come out and play with passion, be physical and disciplined and we'll go in and get a win."