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Decimated defense leaves 49ers without blueprint for success

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In the offseason, the 49ers weren’t shy about the formula they’d use to win some games in 2016.

They’d play relentless defense, they’d pound the football with Carlos Hyde and they’d let Blaine Gabbert do just enough to keep them in games. Hopefully, that would be good enough to hover around .500.

Plans can be blown into smithereens in the National Football League.

After a 1-3 start, the 49ers’ defense is not the backbone of the team many anticipated. The unit is dead last in the league in stopping the run (140.0 yards per game), and 26th total in total defense. There’s a golden rule in football: If you can’t stop the run, you can’t be a good defense. Cowboys rookie Ezekiel Elliot was the latest to victimize San Francisco’s defense, and mimicked eating a spoon after galloping for several big runs.

What’s scary is that this is nowhere near rock bottom.

NaVorro Bowman’s foot injury is expected to be severe, if not season-ending. Besides being the best player on the roster and a key veteran leader, Bowman is the most critical player used to stop the run as the Mike linebacker. The slew of running backs the 49ers face next: Arizona’s Davis Johnson, Buffalo’s LeSean McCoy and Tampa Bay’s Doug Martin. Michael Wilhoite and Gerald Hodges have a crater sized hole to fill in the middle and the bleeding is just beginning.

What’s damning, is that the defense in particular was supposed to be the saving grace for this transition season. GM Trent Baalke’s last four first round picks were all on that side of the ball, and all good players. Eric Reid, Jimmie Ward, Arik Armstead and DeForest Buckner were supposed to surround Bowman for a 2.0 version of a unit that carried the franchise deep into the postseason under Jim Harbaugh.

And that’s the troubling concern here. The individuals are talented, but the collective whole is not.

There’s a flaw in San Francisco’s defensive scheme Pro Football Focus pointed out. The Cowboys averaged just 3.4 yards per carry when defensive coordinator Jim O’Neil used his base packages. But when the 49ers lined up in the nickel, Dallas spread the field as was able to rush for 6.5 yards per carry. You could call that getting out-coached.

A year ago, Browns players privately complained to me about O’Neil’s scheme in Cleveland. Stopping the run was a confusing process. Players were lined up in different spots all across the field to try and cause pre-snap identification problems, but then found themselves in poor positions to bring running backs down. Gap integrity wasn’t what the run defense was founded upon. Instead, defensive linemen were supposed to create chaos and linebackers were supposed to scrape clean through the blocks. Often, it didn’t work that way.

To be clear, 49ers players have not complained about O’Neil’s scheme this year. Bowman, Reid and Ahmad Brooks have all spoken highly of the play calling. There was that Week 1 hallmark shutout against the 3-1 Rams. Players were bought-in from the moment training camp started. The secondary has been mostly solid, ranking 13th in the league (249.5 yards per game). Aaron Lynch will return this week from a suspension to bolster the pass rush and rookie Rashard Robinson was tremendous in his starting debut at cornerback.

But it’s worth reassessing why this 49ers defense isn’t playing up to its potential. Nobody would argue this unit had a talent issue walking into the season. Had they turned in a better performance against the severely undermanned Cowboys, we might be talking about a 2-2 team primed to upset the Arizona Cardinals.

For the first time since 2005 the 49ers have given up more than 400 yards in three straight weeks. And there’s really no telling when this 400-yard streak will definitively end.