National Football League

Retracing How the 49ers Went from Jim Tomsula and Trent Baalke to Kyle Shanahan and John Lynch

Updated Mar. 4, 2020 6:53 p.m. ET

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Fansided, Peter Panacy/FanSided via Niner Noise

Feb 9, 2017; Santa Clara, CA, USA; San Francisco 49ers head coach Kyle Shanahan speaks to the media between general manager John Lynch and chief executive officer Jed York during a press conference at Levi’s Stadium. Mandatory Credit: Kelley L Cox-USA TODAY Sports

The San Francisco 49ers hired their third head coach in as many years in Kyle Shanahan and also replaced longtime general manager Trent Baalke with John Lynch. Niner Noise takes a step-by-step look at from where the 49ers came to how they got here.

If only San Francisco 49ers fans could know then what they know now.

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The Niners hired the hottest head coaching commodity on the open market this offseason, Kyle Shanahan, and also went out of the box to bring in general manager John Lynch.

Not long ago, San Francisco’s hopes hinged on a controversial GM with tenure, Trent Baalke, and a relatively unheard-of Jim Tomsula as head coach.

My, how times have changed.

Who knows how this new tandem will work out. But it’s safe to say Niners fans are far more enthusiastic about this pairing than any with Baalke, Tomsula or even last year’s head coach Chip Kelly.

So how did we get here?

Niner Noise takes a look back to the tail end of the 2015 season when Tomsula was dismissed from his duties. We’ll trace as many steps as possible between that particular moment leading all the way up to Shanahan and Lynch’s hiring in Santa Clara.

So let’s jump in our Niner Noise time machine and head back to January of 2016.

Dec 27, 2015; Detroit, MI, USA; San Francisco 49ers head coach Jim Tomsula during the third quarter against the Detroit Lions at Ford Field. Mandatory Credit: Tim Fuller-USA TODAY Sports

January 4, 2016 — 49ers Fire Jim Tomsula

A season removed after former head coach Jim Harbaugh’s “mutual” parting of ways with the organization, the 49ers decided the one-time defensive line coach, turned head coach, Jim Tomsula wasn’t the right fit.

Tomsula was dismissed after a 5-11 finish. And even though he had the issue of dealing with a roster decimated by all those 2015 departures, Tomsula certainly wasn’t cut out to be a head coach at the NFL level at that time.

He was set up to fail, as Niner Noise described shortly after his dismissal.

Sure, the move was considered the right one at the time. But it’s impossible to put all the blame squarely on his shoulders.

In turn, San Francisco also lost one of its best positional coaches. And that would hurt a year later.

All of that pointed to general manager Trent Baalke.

January 20, 2016; Santa Clara, CA, USA; Chip Kelly addresses the media in a press conference after being introduced as the new head coach for the San Francisco 49ers at Levi’s Stadium Auditorium. Mandatory Credit: Kyle Terada-USA TODAY Sports

January 14, 2016 — 49ers Hire Chip Kelly as Head Coach

In an attempt to reinvigorate what had been a stagnant offense under former head coach Jim Tomsula, CEO Jed York and Co. thought it wise to bring in an offensive mastermind.

That man was former Philadelphia Eagles head coach Chip Kelly.

Kelly came with a stained reputation though. Sure, his first two seasons in Philadelphia produced 10-win campaigns. But his final year, 2015, saw a shakeup of the Eagles roster, largely under Kelly’s direction.

Trent Baalke would still have roster control. That was seen as a good thing, of course. And yet questions about Kelly’s uptempo pace hindering the team’s defense couldn’t be ignored.

The defense would hurt as a result.

Feb 18, 2015; Indianapolis, IN, USA; San Francisco 49ers general manager Trent Baalke speaks at a press conference during the 2015 NFL Combine at Lucas Oil Stadium. Mandatory Credit: Brian Spurlock-USA TODAY Sports

Trent Baalke’s Actions in Free Agency (March 2016) and the NFL Draft (April 2016)

Once CEO Jed York dismissed Jim Tomsula after just one year, it was clear former general manager Trent Baalke was safe.

For the time being.

Baalke knew the 49ers roster needed a complete overhaul. And yet Baalke’s biggest free-agent signing was offensive guard Zane Beadles.

That was about it.

Sure, Baalke never was a big player on the free-agent market. But armed with a tremendous amount of cap space, one had to wonder if the lack of action would come back to haunt San Francisco during the season.

It did.

As far as the NFL Draft was concerned, Baalke cashed in with the Niners’ first-round selection of defensive end DeForest Buckner. And Baalke might have found a gem in cornerback Rashard Robinson (Round 4).

The rest? Well, maybe defensive end Ronald Blair will be a nice addition. Same goes for offensive guard Joshua Garnett, but we’ll see.

Overall, Baalke didn’t have the home-run draft class the team so desperately needed. And this surely put the former GM on the hot seat.

Sep 25, 2016; Seattle, WA, USA; San Francisco 49ers free safety Eric Reid (35) and quarterback Colin Kaepernick (7) and outside linebacker Eli Harold (58) take a knee during the national anthem before kickoff against the Seattle Seahawks at CenturyLink Field. Mandatory Credit: Joe Nicholson-USA TODAY Sports

August 26, 2016 — Colin Kaepernick’s Protest Is Noticed

According to NFL Network’s Mike Garafolo, quarterback Colin Kaepernick’s national anthem protest actually began the first preseason game of the 2016 year.

But it wasn’t until Niners Nation’s Jennifer Lee Chan posted this photo of Kaepernick sitting during the anthem just before San Francisco’s third exhibition:

Kaepernick’s protest certainly gained headway quickly and became a discussion point across the league and beyond.

In house, the 49ers did their best to support Kap. The team made contributions to various charities the quarterback supported. And he received further support from teammates and coaches alike.

Deep down though, one can only think how then-general manager Trent Baalke felt, considering his thoughts on Kaepernick were low to begin with.

Oct 16, 2016; Orchard Park, NY, USA; Buffalo Bills defensive end Jerry Hughes (55) tries to tackle San Francisco 49ers quarterback Colin Kaepernick (7) in the end zone during the second half at New Era Field. Buffalo beat San Francisco 45-16. Mandatory Credit: Timothy T. Ludwig-USA TODAY Sports

November 6, 2016 — 49ers Start 1-7

So much for the 28-0 shutout of the Los Angeles Rams in Week 1 of Monday Night Football.

San Francisco began what would end up the longest losing streak in franchise history — 13 games. All the while, the Niners defense was being gouged on the ground, which points back to the loss of former defensive line coach/head coach Jim Tomsula.

And it didn’t help the 49ers lacked any sort of offensive playmakers either.

Then-head coach Chip Kelly did what he could, most notably replacing an ineffective quarterback Blaine Gabbert with Colin Kaepernick after Week 5.

Remember how Kelly later noted it was one of the only depth moves the team could make? Well, we had our first taste of discontent between Kelly and Baalke.

It helped, but not much. Even when the Niners managed to get leads in games, San Francisco’s defense gave way all too easily in the second half.

Kelly’s unique offense, lacking playmakers or depth, sputtered out after halftime too.

Aug 20, 2016; Denver, CO, USA; San Francisco 49ers cornerback Will Redmond (23) prior to the game against the Denver Broncos at Sports Authority Field at Mile High. Mandatory Credit: Isaiah J. Downing-USA TODAY Sports

November 8, 2016 — Cornerback Will Redmond (ACL) Isn’t Activated

This, perhaps among a number of things, could have been the biggest factor in determining Trent Baalke wasn’t going to be with San Francisco beyond 2016.

Baalke drafted cornerback Will Redmond, who was coming off an ACL tear (where have we heard that before), in Round 3 of the 2016 NFL Draft. The general manager fully expected Redmond to be ready for training camp, per Eric Branch of SFGate.com.

That didn’t happen. And it didn’t happen when the deadline to activate an injured-reserve player to the 53-man roster passed either.

Baalke whiffed on a third-round pick. This hurt, both the 49ers’ chances to rebound down the stretch and Baalke’s prospects to remain employed.

Considering how many other needs the Niners had entering 2016, all one needs to do is look at Redmond’s situation and realize Baalke’s tenure was coming to a close.

Nov 20, 2016; Santa Clara, CA, USA; San Francisco 49ers general manager Trent Baalke before the game against the New England Patriots at Levi’s Stadium. Mandatory Credit: Kelley L Cox-USA TODAY Sports

January 1, 2017 — 49ers Finish 2-14, Fire Trent Baalke and Chip Kelly

The 49ers wrapped up their 2016 campaign with a 25-23 home loss to the Seattle Seahawks and an ugly 2-14 season to add to their franchise archives.

2016 marked a year in which San Francisco set historically bad numbers in yards allowed (6,502), points allowed (480) and rushing yards allowed (2,654), as Matt Barrows of the Sacramento Bee pointed out:

Trent Baalke and Jim Tomsula had to go, right?

They did, shortly after the game’s conclusion. And San Francisco was set to have its fourth head coach in as many years and the first general manager since Baalke took over the job in 2011.

Feb 9, 2017; Santa Clara, CA, USA; San Francisco 49ers general manager John Lynch and head coach Kyle Shanahan during a press conference at Levi’s Stadium. Mandatory Credit: Kelley L Cox-USA TODAY Sports

February 23, 2016 — Kyle Shanahan and John Lynch Officially Introduced

CEO Jed York wasn’t going to look for a stopgap fix to get the 49ers back on track. And some might even question his methods, which isn’t hard to do.

The 49ers had ties to, and interviewed, a number of head coaching candidates. But it was clear the search was boiling down to two — New England Patriots offensive coordinator Josh McDaniels and Atlanta Falcons OC Kyle Shanahan.

We know who won out, by the way.

But the general manager search was a little more provocative. San Francisco also had ties to various candidates here. Turns out, the one person selected — former Fox analyst John Lynch — was completely off the radar.

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He wanted it that way. It was a test to see if the always-leaking 49ers franchise could keep a lid on things. They did. Lynch was hired.

And now we’re here, at the point where Lynch and Shanahan are working to quickly assemble a staff and gear up for free agency and the NFL Draft — points where former GM Trent Baalke missed in recent seasons.

Simultaneously, Niners fans have a feel-good feeling knowing the franchise has turned the page on what otherwise might be considered a forgettable era.

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