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Will the 49ers defense take the step forward we thought they would?

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The San Francisco 49ers defense was expected to take a step forward in 2016. We saw positives in Week 1, but they took a step back in Weeks 2 and 3. Third down is one of culprits.

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Defense has been the prevailing theme of the NFL’s opening three weeks of play. Unblemished early records for teams like the Eagles, Ravens, and Vikings have been fueled largely by top-five performances from the defensive side of the ball, while efforts to slow down the opposition for 0-for teams like the Bears, Browns, and Saints have been futile.

Defense was supposed to be the strength of this 49ers team in 2016. Not in a one-of-the-best-defenses-in-football sense, but in a clear-bright-spot-on-a-rebuilding-team sense. With minimal roster turnover from a 5-11 squad that was actually worse than its record would suggest in many ways, San Francisco’s plan (There is a plan, right?) for the next step of this slow rebuild appeared to revolve around installing a competent offensive coaching staff and banking on the development of the myriad defensive players added to the roster in recent years.

The most valuable resources for a rebuilding team are their day-one and day-two draft picks. San Francisco has made 15 of these premium selections since 2013, and 10 of them have been defensive players, including all four of their No. 1 selections. Six more have been added in the fourth and fifth rounds. Of those 16 players, all but Chris Borland and Corey Lemonier are currently on the 49ers roster, and no fewer than 10 were expected to play a notable role entering the season. All that is to say, this isn’t a defense built around late-round fliers and free-agent cast-offs—significant, meaningful capital has been invested in building up this defense, and 2016 was supposed be the year dividends were paid.

Results after three weeks have been mixed at best. A dominant season-opening performance (Maybe they just need to play while half the country is asleep every week?) was followed by a pair of clunkers on the road against two of the NFC’s best teams. The numbers aren’t awful. San Francisco ranks ninth in defensive DVOA (currently sans “D” until opponent adjustments are added next week), eighth in yards allowed per drive (26.6), 16th in points allowed per drive (1.93), and fifth in drive success rate, which measures the percentage of down series resulting in a first down or touchdown.

Early in the season, however, these numbers are easily skewed by an outlying performance. Here’s a look at how some of those numbers are split between San Francisco’s wins and losses (ranks are where the 49ers would land had they maintained that performance across all three games).

Statistic Week 1 Rank Weeks 2-3 Rank
DVOA -65.3% 1 13.4% 27
Yards/Drive 11.62 1 35.04 23
Points/Drive 0.0 1 3.19 32

Uhh, that’s quite the difference. Over the rest of the season, the 49ers are unlikely to be either the best defense in football or one of the worst, but where they fall on that spectrum is important.

Quality of opposition is certainly a major consideration when looking at those splits. Los Angeles is quarterbacked by Case Keenum and coached by Jeff Fisher, which is maybe the league’s foremost one-two punch of offensive futility. Carolina and Seattle, on the other hand, possessed two of the best offenses in football a year ago and were expected to remain there in 2016 (though Seattle had been awful offensively in the first two weeks).

With that said, the driving force behind San Francisco’s poor defensive play over the past two weeks has been a complete inability to get off the field on third down, even when they had done their job on early downs to set up third-and-long.

Early in the down and distance, the 49ers have actually been solid across all three games, currently ranking 12th in DVOA on first down and fifth on second down, per the Football Outsiders premium database. Third down, however, has been the stuff of nightmares over these past two games. After allowing 2.2 yards per play and a 23.5 percent conversion rate on third and fourth downs (both would rank as the best marks in football) versus the Rams, those numbers skyrocketed to 10.1 and 55.2 percent, respectively, when traveling to Carolina and Seattle.

The most concerning thing about those figures is the alarming rate at which the 49ers are allowing conversions on third-and-long. The switch appeared to flip around halftime of the Panthers game. Cam Newton & Co. converted 5-of-9 third down attempts in the second half on their way to turning a one-score halftime lead into a three-score blowout, including conversions on third-and-7 and third-and-8 on their first two possessions of the second half, both of which ended in touchdowns.

The situation turned silly in Seattle. After a quick-strike touchdown drive to open the game, the Seahawks converted a third-and-10 or longer on each of their next four scoring drives. Every single one of those conversions—which required 10, 15, 14, 17, and 21 (via penalty) yards to convert—came before the Seahawks were in scoring position. By the end of those drives, it was midway through the third quarter, Seattle had a commanding 27-3 lead, and the game was long over.

Equally important is how these conversions happened, especially considering San Francisco’s coming opponents (more on that in a moment). Russell Wilson consistently took advantage of 49ers’ lapses in the middle of the field.

On their second possession of the game, a pair of penalties put the Seahawks in second-and-21, with a six-yard Christine Michael run leaving them in third-and-15. Seattle goes empty on the play, and Jim O’Neil’s squad counters with man-free—man-to-man coverage with a single deep safety and usually another safety or linebacker (sometimes both) underneath as a “hole” defender—which has been the dominant coverage for the 49ers this season.

One of two problems seems to occur here. Either NaVorro Bowman, who is aligned over Jimmy Graham pre-snap, is supposed to carry Graham vertically up the seam, or Eric Reid does an awful job of providing help over the top if he knows Bowman is going to settle underneath. If the intent was to bracket Graham, which seems like a reasonable possibility, Reid should be breaking on that route from his deep alignment almost immediately after the snap to take away the seam throw. None of that happens and the result is one of the easier third-and-15 conversions you’ll see.

One quarter later, with the game not yet out of hand, San Francisco manages to out-do themselves. O’Neil calls what effectively amounts to a prevent look on third-and-14: three-man rush, five underneath defenders sinking to the first-down marker, and three deep defenders. Despite a 12-yard cushion and ample underneath help, Tramaine Brock sits too hard on the out-breaking route to the sticks and Doug Baldwin—who basically looked like Antonio Brown: West Coast Edition in this game, catching 8-of-10 targets for 164 yards and a score on seven (!) different defenders—blows passed the veteran corner for a 59-yard reception. Wilson would connect with Graham for an 18-yard score, also in a vacant middle of the field, on the ensuing play and the rout was on.

For context, NFL teams have converted just 23.2 percent of third down attempts requiring 10 or more yards since the start of the 2015 season; Seattle converted 83.3 percent of these attempts (5-of-6) last week. Had the 49ers been able to get off the field at a league average rate in these situations, suddenly the makeup of this game is considerably different. Given the way the 49ers offense played, it’s certainly not enough to suggest they should’ve walked out of this game with a victory, but it’s the difference between an encouraging road performance against a division rival and another embarrassing loss in Seattle.

These problems don’t bode well for upcoming games against the Cowboys and Cardinals. Carson Palmer torched San Francisco’s defense in the middle of the field a year ago, and will test their secondary downfield much like Wilson did. Arizona’s offense is off to a rocky start, but you could’ve said the same thing about Seattle a week ago, and the 49ers proved to be the catalyst needed to get on the right track.

Dak Prescott and the Cowboys are having no such troubles offensively, ranking fifth in pass efficiency and third in run efficiency so far this season. Dallas has converted 54.5 percent of third down attempts this season, trailing only the Broncos. And as Pro Football Focus detailed this week, Prescott’s success through three games has had a lot to do with his ability to throw accurately to the middle of the field.

Cole Beasley and Jason Witten have been the primary benefactors of Prescott’s proficiency between the hashmarks, with Beasley looking especially impressive thus far while posting the league’s third-best yard per route run average (2.77) among slot receivers through three games, per Pro Football Focus. Top wideout Dez Bryant is doubtful to suit up this week, leaving Beasley and Witten responsible for carrying the bulk of the workload in the passing game. Considering the games Baldwin and Graham just had in Seattle, that’s not exactly a promising sign.

Long-term projections for San Francisco’s defense are a bit more optimistic. Four of the next five games are at Levi’s Stadium, where the 49ers defense has played markedly better dating back to last season. More importantly, teams who perform well on first and second down tend to see their third-down performance fall in line over a larger sample. If the 49ers can clean up some alignment issues and continue to perform well on early downs, we should eventually see their third-down effectiveness follow suit, even if that doesn’t happen in Week 4.

Finding some semblance of a pass rush should help. Getting Aaron Lynch back next week is obviously a plus, but O’Neil is almost certainly going to need find ways to manufacture pressure via the blitz, similar to what Arizona has been forced to do in recent seasons without a premier edge rusher.

Three games is hardly enough to reach any final conclusions on the 49ers defense in 2016, but there’s no denying this is an important season in the development of this group. Significant resources have been spent rebuilding this defense in hopes that they can eventually approach the success seen under former defensive coordinator, Vic Fangio. It’s too early to expect them to reach that level this season, but a discernible step forward from their bottom-six performance in 2015 is needed. And if that’s going to happen, correcting their issues on third down is the place they’ll need to start.

*Note: Unfortunately, some time constraints prevented me from getting to 5 things I like and don’t like this week, but it will be back next week.