What’s wrong with the previously vaunted 49ers defense? A level-by-level breakdown

The Niners looked helpless at times against the Cardinals' backups Sunday afternoon.

Watching one of the 49ers’ worst defensive showings in years prompted me to quiz coach Kyle Shanahan exactly why it happened.

“We’ve got to find out,” Shanahan replied after Sunday’s 31-17 loss to Arizona. “It was extremely disappointing.

“I don’t think we tackled very well. I didn’t think we had 11 guys swarming to the ball enough. I think we made it pretty easy on those guys.”

Here’s what I think: The 49ers defense lacks discipline. Players are missing their assignments, veering out of their lanes, committing untimely penalties and not “swarming” to the football, as first-year defensive coordinator DeMeco Ryans vowed they would.

Missed tackles have ensued. That also was the case in the 49ers’ opening two seasons under former defensive coordinator Robert Saleh.

Remember those 125 missed tackles in 2017? More of the same came in 2018 before they improved, eventually emerging as a dominant defense to trigger the 2019 team’s Super Bowl run.

All that defensive equity has vanished, as evident when the Cardinals’ “B team” ravaged the 49ers. Or when Aaron Rodgers did it in the final 37 seconds. Or when Jonathan Taylor, Justin Fields and James Conner each ran for triple-digit yardage over the past three weeks.

The 49ers’ penalty woes were reflected by an NFL-high 14 pass-interference calls through six games. Josh Norman’s taunting penalty Sunday, after a third-down stop, showed just how exasperating these defensive misfits have become.

My follow-up question to Shanahan on Sunday: Do you ever give them a piece of your mind during games or do you just leave that to Ryans?

“I talk to the coaches throughout the game, but no, I don’t bring the defense together on the sidelines and give some big speech,” Shanahan replied. “I don’t do that for the offense, either.”

Well, gather around, fellas. It’s time to further analyze why the defense is flailing and how they must change the second half of this fading-fast season:

DEFENSIVE LINE

What’s gone wrong?

Nick Bosa can’t do it alone, though he’s sure tried. Playing a remarkable 73 percent of the snaps a year removed from knee reconstruction, Bosa has seven sacks, 17 quarterback hits and 12 tackles for loss that are tied for the NFL lead.

Unlike Bosa’s rookie year, he lacks play-making companionship on that frontline. Javon Kinlaw has succumbed to season-ending knee surgery, Dee Ford’s bad back acted up to put him in familiar limbo, and the 49ers haven’t received any edge-rushing boost from newcomers Samson Ebukam and Arden Key.

D.J. Jones has been OK (five tackles for loss) but Kentavius Street hasn’t accelerated his game while playing the same 40 percent of snaps as last season.

Arik Armstead, as often through his career, is a popular target of critics. He only has two sacks and three tackles for loss, but he’s having a decent year – in a season when the 49ers need more from him, which now must take place on the interior.

What must change?

Matthew Stafford is leading the Rams (8-2) into Levi’s Stadium on Monday night, and the 49ers urgently need a better pass rush to keep him from annihilating a porous secondary. That means, as Bosa crashes from one side, the 49ers need pressure from the other edge (Ebukam, Key, Jordan Willis) but also up the middle from Armstead, Street, Jones and Kevin Givens.

If the 49ers are to improve their 26th-ranked run defense, that must start in the trenches, where Kinlaw won’t be returning for a year from his recent ACL repair. So, Jones, Street and Givens must step up in their contract years, and the interior onus is on them (plus Armstead) while Maurice Hurst (calf) is likely out a couple of more weeks.

Who is the ‘X’ factor?

Ebukam. His only sack this season came on third down to help clinch a win in Chicago. With Ford shelved again, it’s on Ebukam to produce more than he has in 229 snaps.

LINEBACKER

What’s gone wrong?

No, Fred Warner didn’t take the money and run the wrong way. His high-priced extension was warranted, and as he explains twice a week to the media why the defense is struggling, he’s taking accountability for his own faults. If Warner is overthinking things, it’s likely because he’s missing his wingman, Dre Greenlaw, who’s been out since adductor surgery following a Week 1 pick-six.

Azeez Al-Shaair is too often caught out of position, is not a sound tackler and is not as slick in coverage as his speed would indicate. Warner has 75 tackles to Al-Shaair’s 52.

With Al-Shaair covering Greenlaw’s spot at weak-side linebacker, converted safety Marcell Harris has filled in at strong-side linebacker, and while Harris has played through a thumb injury in recent weeks, his habit of missing a tackle a game has not been corrected.

What must change?

Stop allowing rushing touchdowns. They’ve yielded 12 total, and at least one each game, with a season-high three last Sunday.

Compare that to these season totals: eight in 2017, ’19 and ’20, and nine in 2018. The 49ers did not allow a rushing touchdown the first 14 games in 2011 – a long decade ago.

Warner needs to make more plays as a First-Team All-Pro. He’s yet to force a turnover, and Ryans isn’t sending him or other linebackers enough on blitzes to rattle quarterbacks.

Obviously, the linebackers need to tackle better, and do so by pushing back ballcarriers rather than letting them fall ahead for a couple of extra yards. Punching the ball out along the way is a must, too, with only three fumble recoveries this season.

Who is the X-factor?

Greenlaw is expected to resume practicing this week, though that doesn’t assure him an immediate spot in Monday night’s game. Regardless, the 49ers need his “Big Play Dre” flair on defense.

CORNERBACK

What’s gone wrong?

Everything. Jason Verrett’s season-ending knee injury in the opener waylaid this unit out the gate, even though the 49ers should have known his health wouldn’t be a sure thing.

Pass-interference and holding penalties amplify how the cornerbacks are panicking when caught out of position, and the lack of interceptions shows how they’re not looking for the ball or attacking it in the air.

Personnel moves also are highly suspect. They’ve gone with veterans Josh Norman and Dre Kirkpatrick rather than allow rookies Deommodore Lenoir and Ambry Thomas to learn on the job. Incumbents Emmanuel Moseley and K’Waun Williams haven’t played inspiring football, though Williams flashed his ability with the third-down stop Sunday that eventually led to Norman’s taunting penalty.

Aside from the 2021 draftees Lenoir and Thomas, the rest of the cornerbacks are short-timers, and they’re not coming through as the mercenaries needed.

What must change?

Create takeaways, not penalties. Make a play on the ball, not the receiver. Make quarterbacks fear at least some aspect of launching deep balls, and make it harder on NFL officials to watch for incidental contact they’ll flag.

Norman’s rib injury (and taunting fallout) could keep him on the bench and open the door again for Lenoir or Thomas to ramp up their rookie seasons and learn on the fly, finally.

Who is the X-factor?

Take your pick between Lenoir or Thomas. Lenoir showed promise early but hasn’t played a defensive snap since Week 3; Thomas’ only nine defensive snaps came in the opener.

SAFETY

What’s gone wrong?

Even before Jimmie Ward and Jaquiski Tartt got familiarly injured, the last line of defense was not imposing, not when quarterbacks went deep each game against cornerbacks who often lacked safety support. Neither Ward nor Tartt has forced a turnover, and each has only defended one pass.

Second-string safeties Talanoa Hufanga and Tavon Wilson struggled mightily against the Cardinals. Hufanga’s passion is admirable, but his lack of elite speed will hinder his development. Wilson (foot) is likely heading for injured reserve, so depth is a concern.

What must change?

Ward (quadriceps) and Tartt (knee bruise) eventually will return and ideally bring stability to a volatile unit. No hot-shot safety is waiting in the wings to pair with Hufanga, but perhaps Tony Jefferson II or Will Parks will come up from the practice squad and revitalize their careers.

Who is the X-factor?

Hufanga is the dream choice, as if his rookie year will suddenly transform him into an all-around star. However, the bigger upshot could come from Ward, if he gets healthy and finally gets the license to freelance as he envisioned in Ryans’ supposedly more aggressive scheme.