What I'm seeing from the San Francisco 49ers: Missing ingredient sticks out like sore Achilles

SANTA CLARA, Calif. — It doesn’t require much to get fingers hovering over the panic button in San Francisco. And after a pair of September losses, there were a lot of hands inching in that direction.

A win over the New England Patriots has calmed the nerves a bit, but the San Francisco 49ers certainly didn’t look like the juggernaut they were for most of the 2023 season in that game, either.

What can we assess after four games? What are they lacking? What are the positions of concern and areas of hope? Here are a few observations at the almost-quarter mark:

49ers obviously are missing a certain someone

The biggest takeaway after four games is that the 49ers are a different team than the one that started out the 2023 season on a five-game winning streak, especially on offense.

Last year’s squad was ultra-efficient in the red zone, it gobbled up YAC yards in chunks and threw a lot of passes to the tailback. The 2024 version? It ranks 20th in red zone efficiency, 31st in YAC yards per reception and seems reluctant to throw to Jordan Mason out of the backfield.

Last year’s leading scorer was Christian McCaffrey. So far this year it’s Jake Moody — by a wide margin. He’s already kicked 11 field goals, more than half his total (21) last season.

The missing element? It’s sticking out like a sore Achilles. McCaffrey’s absence underscores just how essential he was to the 2023 offense, especially around the goal line. At this point last season he’d already scored seven touchdowns.

The 49ers have been reluctant to offer any sort of timeline for the tailback’s return. They have stressed, however, that they’ll be cautious with his ramp-up, suggesting that it might be another month or so before he’s back. If that’s the case, the storyline for the first half of the season will be how the 49ers have adjusted and evolved to life without McCaffrey.

What does future look like for Jordan Mason?

Yes, this is very much a first-world NFL problem. But what happens to Mason if/when McCaffrey is back in the lineup? As it stands, Mason is the league’s second-leading rusher and it’s hard to fathom where the 49ers would be without his steady running.

Do they make him an every-third-series rusher when McCaffrey is back? Do they make McCaffrey, the reigning Offensive Player of the Year, a mere change-of-pace back or third-down specialist?

The 49ers might be able to line up both in the backfield at the same time. They did so with some success during a brief interval in 2022 when Jeff Wilson Jr. and McCaffrey were on the same squad. That worked well because both were good at catching passes out of the backfield. Mason isn’t nearly the same threat as a receiver, which might telegraph San Francisco’s intentions in a two-back situation.

Having both in at running back also would send the best, most versatile fullback in the league, Kyle Juszczyk, to the sideline. (Like we said: first-world problems).

Edge seems sharper, but let’s wait and see

Defensively, the 49ers appear to have made strides from last season when their two biggest problems were 1) a lack of pressure off the edge from players not named Nick Bosa and 2) a steep drop-off in coverage as soon as their No. 3 cornerback took the field.

As it stands, Bosa leads the team with 19 quarterback pressures followed by his bookend, Leonard Floyd, with 11. This situation, however, will require further scrutiny. Six of Floyd’s pressures came in Week 4 against a rickety Patriots offense that’s allowed the second most sacks in the league, and he looked rather flat in losses to the Minnesota Vikings and Los Angeles Rams. If the Patriots game is the outlier, general manager John Lynch might have to beat the bushes for defensive end trades for the second straight season.

When it comes to the third cornerback, the team is shifting from veteran Isaac Yiadom to rookie Renardo Green. There are bound to be growing pains, but having Green as the No. 3 cornerback puts the three most talented cornerbacks on the field at the same time. How the 49ers match up against the Seattle Seahawks’ top three receivers — DK Metcalf, Tyler Lockett and Jaxon Smith-Njigba — in Week 6 ought to be fascinating.

Intrigue at defensive end

A person of interest for the month of October: Sam Okuayinonu (pronounced: OH-koo-AH-nu).

He’s definitely been their fourth-best defensive end through four games and might be their third-best player at the position now that Yetur Gross-Matos is playing roughly half the time on the inside. Okuayinonu, who nearly made the 53-man roster coming out of training camp, was promoted to the 53-man squad last week.

He was born during Liberia’s civil war and lived there until he was 12. He readily admits he’s still learning about football, which he didn’t start playing until he was a high school senior. He joked that he probably annoys Bosa by constantly asking him questions about his craft.

Said Bosa in reply: “I love when guys ask me questions. I don’t have it figured out myself, but I have a few things figured out. He sits right next to me in meetings and he’s always asking me stuff.”

All of which is to say that Okuayinonu, 26, has plenty of upside. His football inexperience and lack of length — he’s 6-1 — help explain why he went undrafted in 2022. But he’s got long arms (33 1/2 inches) and a powerful lower half, a combination that can work on the edge in the NFL. The similarly sized Shaq Barrett, for example, had 59 sacks in nine NFL seasons. The Philadelphia Eagles’ Brandon Graham, another 6-1 defensive end, has 74 career sacks.

Rookies already making waves

A typical Week 4 sentence about a rookie might be: “Rookie A played the first regular-season snap of his career Sunday.” Guard Dominick Puni? He missed the first regular-season snap of his career Sunday. Puni was shaken up on the 49ers’ second offensive play but jogged off the field and was back for the fourth. He’s already played 275 snaps, which is roughly a third of what the 49ers’ 2023 draft class — nine players in all — logged on offense and defense last season.

The other members of Puni’s draft class have accounted for 159 offensive or defensive snaps with another 19 coming from undrafted defensive tackle Evan Anderson on Sunday. The bulk of those snaps are from safety Malik Mustapha, who started against the Patriots. Mustapha will return to a backup role when Talanoa Hufanga is back from a minor ankle injury, but look for Mustapha in three-safety formations in the coming weeks. The team’s safety group seems stronger than the linebacker position, at least until Dre Greenlaw (Achilles) is ready to get back on the field.

Kyle Shanahan said he and his staff were impressed by the rookie class as far back as the May OTA practices.

“They seemed like a very mature group,” he said. “We didn’t have to teach too many of them how to act like pros as we say. They came in, they knew how to walk through, they worked very hard. The effort was always there. … So I’ve been impressed with that whole group. They’re wiser beyond their years in how they’ve acted.”

And the rookie numbers promise to keep growing as Green takes over the third cornerback role and Isaac Guerendo and Jacob Cowing get worked into the offense. With Ricky Pearsall likely to join the mix in the coming weeks, the class is already shaping up to be one of the team’s best in a while.

(Top photo: Sergio Estrada / Imagn Images)