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SAN FRANCISCO -- The code for San Francisco 49ers to succeed under Jim Harbaugh has not been difficult to crack. It begins with the defense, a unit that is dominating despite playing without All-Pro linebackers Aldon Smith and Patrick Willis. Sure, the 49ers have been pretty spectacular on offense at times. But this team lives and dies with its defense. And if the 49ers stick around as serious contenders in the NFC, it will be because of the defense. After all, it was the defense that a week ago lifted San Francisco out of a two-game funk. And while completely dominating the Houston Texans 34-3 on Sunday night, the 49ers showed the rest of the league that this is still one of the most dominant defenses in the NFL. And that this is still a Super Bowl contender. There was serious concern about the 49ers after they were humiliated by the Seattle Seahawks and the Indianapolis Colts in Weeks 2 and 3. They were outscored 56-10 in those two games. The defense looked tired, and injuries were mounting. Yet it no longer appears to be a crisis situation in San Francisco. The 49ers have responded to those two drubbings by outscoring the Rams (on the road) and the Texans by a combined 69-14. After Seattle lost to the Colts on Sunday to drop to 4-1, the 3-2 49ers are back in the NFC West hunt. And after a tough start, the schedule now softens a bit for the 49ers. They host Arizona next week, and then travel to play the Jake Locker-less Titans and then the winless Jaguars in London before the bye. If the San Francisco defense continues to play well, turning a 1-2 start into a 6-2 record at the bye appears more than realistic. There is no reason to think this defense is going to sag now. It has thrived under adversity. Smith went to an alcohol treatment center on Sept. 24. There is no timetable for his return, but he may not be back until after the Nov. 2 bye. Special-teamer Dan Skuta and rookie Corey Lemonier have played in his place. Willis went out with a groin injury in the Colts’ loss. The team is being cautious with him (he was a game-time inactive Sunday), and barring a setback, Willis might return against Arizona. Meanwhile, Michael Wilhoite has played well in his absence. This has been a theme for San Francisco this year. For a defense that hasn’t rotated much under defensive coordinator Vic Fangio, its depth is really showing. Glenn Dorsey took over at nose tackle when Ian Williams went down for the season in Week 2. Tramaine Brock has been spectacular as the No. 3 cornerback since Nnamdi Asomugha went down with a knee injury two weeks ago. There is little chance Asomugha wins his job back. Sunday’s night’s domination did not come without the potential of more adversity. Standout defensive tackle Ray McDonald left with a biceps injury. He said after the game he will have an MRI on Monday. McDonald would be missed if he is out for an extended period of time. However, his replacement, Tony Jerod-Eddie, had an interception Sunday night after McDonald was hurt. That’s what these 49ers are doing. Backups are producing when the stars are out. To think the San Francisco defense has allowed just 14 points in two games playing without Smith, one of the most dynamic pass-rushers in the game, and Willis, a potential Hall of Famer, is stunning. How many other defenses could thrive without their best players? "That’s why we are here," Skuta said. "You see it in practice. You see guys step up when needed here." Added standout safety Donte Whitner, who had a tremendous game Sunday night: “This defense runs 22, 23 [deep] … it’s one of the deepest defenses in the league. … Yes, we miss our guys, but we still have to get the job done. You saw that tonight.”  The 49ers’ defensive dominance started early Sunday. On Houston's first drive, Brock made the first of his two interceptions against quarterback Matt Schaub and returned the ball 18 yards for a touchdown. It was the fourth game in a row that Schaub had an interception returned for a score. It set the tone for a long night for the Texans' quarterback.
The 49ers forced four turnovers. The 49ers ate Schaub alive on short passes. According to ESPN Stats & Information, Schaub averaged just 4 yards on passes that traveled 10 or fewer yards. All three of Schaub’s interceptions came on short passes. The 49ers scored 34 points and were runaway winners -- and quarterback Colin Kaepernick completed just 6 of 15 passes for 113 yards and a touchdown. San Francisco was in game-management mode because of what the defense was doing. “We look to set the tone on defense,” Wilhoite said. “That’s the plan every week, and it worked out well tonight.” There was a lot of concern about the San Francisco defense when this team was 1-2. It had allowed 84 points in three games. But I thought the point was misleading. The defense sagged late in games and got tired after the San Francisco offense couldn’t muster and sustain drives against the Seahawks and the Colts. Sunday night, the offense, led again by a strong ground game, held up its end of the bargain and again and fed off the defense. That’s how the 49ers win. "I know some people were worried about the defense earlier," Whitner said. "But this is a strong, winning defense. We are showing that."
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