SANTA CLARA, Calif. — The San Francisco 49ers are playing some of their best defensive football of the past decade, and it’s just about the entire unit that’s doing it.

The team is getting contributions from every area on a defense that has climbed to No. 6 this week in the NFL rankings and been largely responsible for a 3-1 start that has the first-place 49ers in early command of the NFC West.
San Francisco recorded its first shutout in 119 games with last week’s 35-0 rout of the St. Louis Rams, the latest testament to how well the unit is grasping defensive coordinator Greg Manusky’s 3-4 scheme.
“After you’ve been around a system for a while, you know exactly what to expect from your other guys and what to expect from me calling the plays,” Manusky said Thursday. “That is a comfort level for everybody. They understand where everybody’s supposed to fit, where everybody’s supposed to be, and they’re flying around doing good things and playing hard, playing physical and playing fast.”
San Francisco’s defense scored as many points as its offense last week as linebacker Patrick Willis returned an interception for a touchdown and defensive lineman Ray McDonald scored after recovering a fumble.
Those kinds of big plays are becoming typical for a unit that ranks sixth or higher in the NFL in eight statistical categories and is second in the league in fewest points allowed per game.
“You can definitely tell we’re on track,” free safety Dashon Goldson said. “It’s all coming together because we believe in this defense and we love to play together. We’re all playing for one another and we know what we can do as a unit. So now it’s all about getting it done.”
The improvement actually began near midseason last year after the 49ers fired head coach Mike Nolan and gave complete control of the defense to Manusky. Nolan often tinkered with the defensive strategy and called for a hybrid attack that used 4-3 sets.
The 49ers finished 13th in the NFL in total defense last season, matching San Francisco’s highest final ranking since the team led the league in defense in 1997.
The defense has built on that finish this year to carry a team that ranks 28th in the league in total offense. A quarter into the season, the 49ers have allowed more than 300 yards and more than 16 points in a game just once.
Willis continues to emerge as one of the NFL’s dominant defenders and combines with veteran Takeo Spikes to give San Francisco one of the most productive inside linebacker tandems in the league.
That pair had 22 tackles and 3.5 sacks last week in a scheme that’s designed for them to make plays. They have been free to swarm to the football because of the play of nose tackle Aubrayo Franklin, who is off to the best start of his career.
“It all starts off with the nose and Aubrayo is having a heck of a season so far,” Manusky said. “The last four weeks he’s been one of the better nose tackles in the league. That’s a position that’s a big focal point in any 3-4 defense. He’s taken the challenge in not only controlling the running game and making tackles, but also keeping guys off Patrick and Takeo.”
The 49ers rank No. 4 in the league in stopping the run. They’ve yet to allow more than 95 yards rushing in a game despite so far facing the likes of reigning NFL rushing champion Adrian Peterson of Minnesota and Steven Jackson of St. Louis.
Now come the Atlanta Falcons and running back Michael Turner, who finished second in the NFL to Peterson last season with 1,699 yards rushing. The 49ers host the Falcons on Sunday in a matchup that will take San Francisco to its bye week.
“Our mindset going into every game is to stop the run,” Franklin said. “If we can get those guys in third-and-long situations, we can control the game. We take it as a challenge as a defensive line to hold guys under 100 yards (rushing) and that’s what we’re going to try to do the rest of the season.”
The 49ers also have been getting solid play from a secondary that has been forcing turnovers and playing well in coverage. San Francisco ranks 10th in the league in pass defense.
“It’s everybody doing it,” Franklin said. “We’re doing the same things we’ve always done and making opponents adjust to us now. We’re playing together and having fun and that’s what we strive for, because we’re only as good as our unit is.”