Aaron Lynch
San Francisco 49ers: An Autopsy of the 2016 Season
Aaron Lynch

San Francisco 49ers: An Autopsy of the 2016 Season

Updated Mar. 4, 2020 8:16 p.m. ET

The 2016 NFL season is coming to a close, and the San Francisco 49ers are wrapping up what has been a forgettable year. Niner Noise performs the autopsy on what went wrong for the red and gold this season.

October 23, 2016; Santa Clara, CA, USA; San Francisco 49ers head coach Chip Kelly (center) talks to quarterback Colin Kaepernick (7) and quarterback Blaine Gabbert (2) during the fourth quarter against the Tampa Bay Buccaneers at Levi’s Stadium. The Buccaneers defeated the 49ers 34-17. Mandatory Credit: Kyle Terada-USA TODAY Sports

A lot of things went wrong for the San Francisco 49ers in 2016.



Ramblin' Fan 1 dColin Kaepernick Helped Plenty of Fantasy Football Owners After Performance Against Rams

More headlines around FanSided:

1 d - 49ers : 5 Options for San Francisco's First-Round Pick2d - Carlos Hyde tears MCL in 49ers Week 16 Victory2d - 49ers Briefly Hold First Overall Pick2d - A Holiday Thank You to Our 49ers Fans from All of Us Here at Niner Noise2d - What San Francisco 49ers fans really want this holiday season — Part 12More News at Niner Noise

And while the 2-13 Niners still have one game left to play, it’s safe to say this year has been nothing short of a disaster.

So what happened?

Niner Noise takes an all-encompassing look at an autopsy, of sorts, for this season’s campaign under first-year head coach Chip Kelly and a swarm of underachieving performances across the roster.

Pick a stat and, most likely, the Niners are at or near the bottom of it. That’s what two-win teams do — fail.

And while there are some positives here and cornerstones to build on, the vast majority of problems in Santa Clara led to the product seen on the field for the better part of 16 weeks.

We can try to narrow the blame, perhaps calling out CEO Jed York or general manager Trent Baalke. But there are way more fingerprints on this year’s 49ers than just a couple of names.

Let’s dive deeper and see just how San Francisco’s 2016 efforts fell apart.

Feb 1, 2016; San Francisco, CA, USA; San Francisco 49ers chief executive officer Jed York during the Super Bowl 50 host committee press conference at the Moscone Center. Mandatory Credit: Jerry Lai-USA TODAY Sports

It All Starts at the Top

This all happened on your watch, Jed York.

As CEO of the franchise, York bears a huge amount of the responsibility associated with yet another losing season in Santa Clara. Remember, York was the primary person responsible with letting former head coach Jim Harbaugh go and ensuring general manager Trent Baalke retained the power.

San Francisco is still reeling from the consequences of that decision two years later.

Nevertheless, the past is the past. Fans can cry murder about Harbaugh’s departure. But what does that solve moving forward?

The problem, as was the case in advance of this season, was the 49ers had no discernible direction or path to get them back to respectability.

Just ask the Santa Rosa Press Democrat’s Grant Cohn, who had no problem indicting York:

You’re the worst owner in sports. Every idea or instinct you ever had about how to build a franchise was wrong and you deserve to be fired. But, you won’t be fired. Not in this game. Your parents own the team and they’re giving you another chance to fix things.

York didn’t know how to fix things. Not then and, in all likelihood, not now.

So it’s simple — how can something come together when the overall architect of the plan has no clue what he’s doing?

April 27, 2012; Santa Clara, CA, USA; San Francisco 49ers head coach Jim Harbaugh and first round draft pick wide receiver A.J. Jenkins and general manager Trent Baalke pose for a photo at the 49ers headquarters. Mandatory Credit: Kelley L Cox-USA TODAY Sports

GM Trent Baalke and Repetitive NFL Draft Failures

Don’t blame general manager Trent Baalke for the mass exodus of talent that left the 49ers in 2015.

Just blame him for not adequately stockpiling anywhere near enough replacements.

    One might argue Baalke had just a single good NFL Draft — 2011. 2012 was a bust. 2013 wasn’t particularly great. And it’s not looking good for 2014 or 2015 either.

    All GMs make mistakes. There’s no perfect science here. But the better general managers and scouts make fewer errors in evaluating and picking talent. Based on the downward trend of San Francisco’s rosters in recent years, it’s easy to point out why Baalke has failed on multiple occasions.

    And no, Trent Dilfer, this isn’t a case of Baalke being an expert on “grocery shopping” and the 49ers coaching staffs the last three years not being adequate “cooks.”

    Take 2013 third-round draftee Corey Lemonier as a perfect example. Baalke moved up to get the linebacker in that particular round. After three-plus years, it was clear he’d never cut it on the 49ers’ already problematic roster.

    He didn’t cut it with the Cleveland Browns either, being released not deep into the 2016 season. So Lemonier has the reputation of being cut by the two worst teams in the NFL this year.

    A wasted Round 3 pick.

    And there are far too many of them.

    Oct 12, 2014; Glendale, AZ, USA; Arizona Cardinals defensive end Darnell Dockett (90) looks on during the second half against the Washington Redskins at University of Phoenix Stadium. Mandatory Credit: Matt Kartozian-USA TODAY Sports

    GM Trent Baalke and Failures in NFL Free Agency

    It would be easy to lump general manager Trent Baalke’s problems in recent years into just one slide. But the NFL Draft shortcomings and inadequate moves in free agency are simply too big to break down that way.

    Baalke has never been a big free-agent player. And that’s fine. Most good teams are built through the draft and only supplemented via free agency. But Baalke’s problems with the draft have put even more importance on free agency.

    Last offseason was a perfect example. The Niners were bad and needed an influx of talent. And yet Baalke’s biggest free-agent acquisition was a subpar guard in Zane Beadles. All the while, the Niners carried over a huge amount of cap space — $42,440,838 currently, per Over the Cap, which ranks second most in the NFL.

    But look back to Baalke’s acquisitions in 2015. The 49ers picked up defensive tackle Darnell Dockett, cornerback Shareece Wright, offensive lineman Erik Pears and wide receiver Torrey Smith, among others.

    Pears was likely slotted to be a swing tackle, so that’s OK. But he ended up having to start in place of retired right tackle Anthony Davis. That wasn’t OK. The rest were intended as regular contributors.

    But Dockett didn’t make the 53-man roster out of training camp, Wright was gone midseason and Smith has endured back-to-back career-low years.

    No, not the best free-agent moves at all.

    Dec 18, 2016; Atlanta, GA, USA; San Francisco 49ers head coach Chip Kelly on the sideline in the fourth quarter of their game against the Atlanta Falcons at the Georgia Dome. The Falcons won 41-13. Mandatory Credit: Jason Getz-USA TODAY Sports

    Head Coach Chip Kelly and Poor Player Development

    Granted, head coach Chip Kelly entered a mess of a situation.

    But he still bears some of the blame despite the context.

    Determining how much is impossible. There is a slew of coaches and assistants who play a role in ensuring a predominantly young and untested 49ers bunch of players.

    Drafting and signing the right players is key. But equally as important is each player’s pro-level development. Needless to say, it hasn’t been adequate.

    A few can break through on talent alone. We know this, and the Niners do have some shining pieces. But others need proper coaching along the way. Perhaps no other league requires this more than the NFL. With 53 pieces all trying to work together to form a fully functioning machine, it’s safe to say Kelly’s efforts this year have fallen short.

    Kelly is responsible for maximizing the talent available. And while that talent is lacking, Kelly couldn’t get the most out of what he had.

    Neither could his assistants. Their efforts fall on Kelly’s shoulders too.

    Nov 30, 2015; Cleveland, OH, USA; Cleveland Browns defensive coordinator Jim O’Neil at FirstEnergy Stadium. Mandatory Credit: Ken Blaze-USA TODAY Sports

    Selecting Jim O’Neil as Defensive Coordinator

    Remember when the 49ers were trying to lure in Houston Texans linebackers coach Mike Vrabel to be the Niners’ defensive coordinator this season?

    Well, finding anyone who’d want to be a DC under a Chip Kelly-led team would be difficult. But it’s hard to say San Francisco had no better options than eventually selecting former Cleveland Browns defensive coordinator Jim O’Neil to fill this role in Santa Clara.

    O’Neil’s defenses in Cleveland ranked No. 32 and 30 against the run in 2014 and 2015, respectively. So it shouldn’t be much of a surprise to see the historically bad Niners defense dead last this year in the same category.

    We can break down O’Neil’s scheme problems. But Rich Madrid of Niner Noise has already done that here, here and here.

    What’s the best way to offset a Kelly offense? It’s to run right at San Francisco’s defense, tire it out and maintain possession.

    And O’Neil’s scheme was the exact worst thing the 49ers could have used to counter this approach.

    The stats speak for themselves.

    October 23, 2016; Santa Clara, CA, USA; San Francisco 49ers wide receiver Torrey Smith (82) runs with the football against Tampa Bay Buccaneers cornerback Brent Grimes (24) during the first quarter at Levi’s Stadium. Mandatory Credit: Kyle Terada-USA TODAY Sports

    A Reliance on Underperforming Players

    Consider all the aforementioned issues, especially roster-related ones, and then factor in the 49ers being forced into a position where they need these guys to be the big playmakers.

    Exactly who are the playmakers on San Francisco’s roster?

    Well, linebacker NaVorro Bowman used to be one before his season-ending Achilles injury. And running back Carlos Hyde could have been one if he had stayed healthy and the team’s offensive line was better at run blocking.

    But the fact is the 49ers don’t have guys against whom other teams have to scheme. Here are a few of the Niners’ “playmakers” and why each simply didn’t contribute anywhere near enough.

    Dec 24, 2016; Los Angeles, CA, USA; San Francisco 49ers quarterback Colin Kaepernick (7) is pressured by Los Angeles Rams defensive end William Hayes (95) as he throws a second quarter pass at Los Angeles Memorial Coliseum. Mandatory Credit: Robert Hanashiro-USA TODAY Sports

    QB Colin Kaepernick

    OK, so quarterback Colin Kaepernick essentially won Week 16 against the Los Angeles Rams by himself. But that’s one game out of the 10 he’s started this season.

    Kap ranks 28th in completion percentage (57.7), 19th in passer rating (88.2) and 27th out of 36 qualifying quarterbacks, per Pro Football Focus.

    Sure, Kaepernick might still possess the athleticism to win a game or two here and there. But he’s also going to make the mistakes that cost games more often than not.

    WR Torrey Smith

    Wide receiver Torrey Smith is a square peg in a round cog, scheme-wise. He’s built for deep routes and taking the top off opposing defenses. But head coach Chip Kelly’s offense isn’t predicated on that. Smith isn’t able to create the separation by the time Kelly wants the ball out of the quarterback’s hands.

    So it’s no surprise Smith’s 2016 campaign set career lows before a season-ending concussion (2015 had already marked career-low numbers prior to this year).

    DE Arik Armstead

    Second-year pro Arik Armstead had a phenomenal training camp and preseason. He was supposed to be the pocket-wrecking force, which allowed San Francisco’s pass-rushers to swarm opposing quarterbacks.

    But a shoulder injury, which eventually cost Armstead the rest of this season, limited Armstead’s ability. Especially against the run.

    Armstead was an OK player at best. Not the dominant force for which Niners fans had been hoping.

    LB Aaron Lynch

    Linebacker Aaron Lynch might want to forget 2016 ever happened. He started off this season with a four-game suspension, was out of shape and missed even more games late, due to an ankle injury.

    Oct 19, 2014; Denver, CO, USA; San Francisco 49ers linebacker Aaron Lynch (59) before the game against the Denver Broncos at Sports Authority Field at Mile High. Mandatory Credit: Chris Humphreys-USA TODAY Sports

    San Francisco’s best pass-rusher has just 10 tackles and 1.5 sacks this year. And this forced the 49ers defense to rely more on fellow linebackers Ahmad Brooks and Eli Harold.

    Neither one of those players were equal to the challenge either.

    Nov 27, 2016; Miami Gardens, FL, USA; Miami Dolphins defensive end Cameron Wake (91) sacks San Francisco 49ers quarterback Colin Kaepernick (7) during the second half at Hard Rock Stadium. The Miami Dolphins defeat the San Francisco 49ers 31-24. Mandatory Credit: Jasen Vinlove-USA TODAY Sports

    No Identity

    Fans knew what kind of team the 49ers were in the 1980s, 1990s and even the early parts of the 2000s.

    Heck, the Niners had a smash-mouth, beat-you-up mantra under former head coach Jim Harbaugh not long ago.

    But that identity is gone. And when Hall of Famer Steve Young called out San Francisco’s ownership on KNBR 680 recently, one of the things he noted was the 49ers’ lack of identity.

    Who are the 49ers? It’s more than just a rhetorical question.

    Is it a team predicated on its defense? Not any longer, no. Are the Niners an offensively driven team with a great running game? Not exactly. Is there an established core of leadership within the locker room? Perhaps, but doesn’t seem to be doing much good.

    The culture-vs.-winning argument is sort of like the “chicken and the egg” take. One can’t exist without the other, but it’s hard to disseminate what comes first.

    Regardless, the Niners lack both. And there’s no signs of it being pointed in the right direction either.

    December 24, 2016; Los Angeles, CA, USA; San Francisco 49ers cornerback Rashard Robinson (33) following the 22-21 victory against the Los Angeles Rams at Los Angeles Memorial Coliseum. Mandatory Credit: Gary A. Vasquez-USA TODAY Sports

    What’s Good with the 49ers and What Can Be Built On

    Autopsies are never fun, even in a sporting context. But rather than leave this on a negative note, let’s take a look at what San Francisco has going for it moving forward.

    December 11, 2016; Santa Clara, CA, USA; San Francisco 49ers defensive end DeForest Buckner (99) during the third quarter against the New York Jets at Levi’s Stadium. The Jets defeated the 49ers 23-17 in overtime. Mandatory Credit: Kyle Terada-USA TODAY Sports

    We’re fortunate to enjoy an NFL league where parity is a rapidly changing thing. Two-win teams can be Super Bowl surprises within a short amount of time. Even if a lengthy 49ers rebuild is likely on the horizon, hope breeds eternal. Nothing stinks forever.

    Perhaps 2016 will be a major eye-opener for CEO Jed York. And while we can talk all about how he and his family care about nothing but money, empty seats and luxury boxes at Levi’s Stadium can’t be a good look.

    Especially considering those lucrative sponsorships.

    So maybe that’s enough to convince York to take a different approach, let someone else handle the football business instead of going with a hands-on approach. Other owners and CEOs do it and with great success.

    More from Niner Noise

      On the field, San Francisco has some pieces too. The Niners are nowhere near as bad as, let’s say, the Cleveland Browns. Up-and-coming players like DeForest Buckner, Rashard Robinson, Joshua Garnett and Jimmie Ward are guys to build around.

      And the 49ers are going to have high draft picks in each round of the 2017 NFL Draft too. That never hurts. Tack on a hopefully aggressive approach in free agency — San Francisco has the money — and things could turn around relatively quickly.

      We’ll have to see. But if there are lessons to be learned from 2016, everyone within the Niners organization nailed down to the floor best pay attention.


      Aaron Lynch
      Get more from Aaron Lynch Follow your favorites to get information about games, news and more