How Colin Kaepernick Lost the 49ers Quarterback Competition

Colin Kaepernick didn’t win the San Francisco 49ers quarterback competition and will start the 2016 NFL season in a secondary role to fellow QB Blaine Gabbert. How did everything seemingly go wrong for Kap in his attempt to resurrect his career?

Blaine Gabbert is going to be your starting quarterback for the San Francisco 49ers and not Colin Kaepernick — the same QB who took the league by storm in 2012 and rode that wave of momentum all the way to Super Bowl XLVII.

Oh, how the risers have fallen.

Kap’s demise from 2012 and 2013 isn’t a new story. And 2015 — the year in which he was benched for Gabbert — marked the former Nevada standout’s worst season in the NFL. This seemingly justified the thoughts Kaepernick’s ascendancy was a mere “flash in the pan.”

But 2016 promised to be different. The 49ers hired head coach Chip Kelly — someone who was intrigued by Kaepernick and whom many felt could resurrect the quarterback’s career.

Well, it doesn’t look as if it’s meant to be. At least not now.

Kaepernick lost the quarterback competition for a number of reasons. Those are worth detailing, because they set up a convoluted context.

Yet the No. 1 reason why Kaepernick will be holding the clipboard to start 2016 is fairly straight forward.

The NFL adjusted to him. Kap didn’t adjust back.

And that’s where things stand. Right now, at least. Kaepernick will be on the sidelines, while Gabbert gets the snaps. Is it an ideal scenario? No. But it’s the reality.

Fall from Grace

To better understand where Kaepernick is now, we have to recall where he was not long ago.

Remember the 49ers playoff run after the 2012 season? Remember the game versus the Green Bay Packers? Yeah, that game.

We don’t need to draw up words or analysis to recall what the league thought of Kap back then. The NFL crew over at Fox Sports did that when it was most relevant:

2013 looked to be the same sort of year. And, not surprisingly, the 49ers made it back to the NFC Championship game for the third consecutive year.

But then 2014 happened. There was tumult between then-head coach Jim Harbaugh and the front office, and Kaepernick looked like, well, a so-so quarterback.

And 2015 was an absolute mess. Kap was benched in Week 9 and then sidelined by a non-throwing shoulder injury.

Injuries hampered Kaepernick’s efforts to bounce back in 2016, and we’ll get to those in a moment. Yet there are far more underlying factors than just a shoulder, knee or thumb injury.

So how about that front office?

Front-Office Fiasco

General manager Trent Baalke will probably never say it, but it’s hard to draw the conclusion he assuredly wants Kaepernick on the 49ers.

Remember that team-friendly deal Kaepernick signed in 2014? Yeah, the one with the various outs worked into the verbiage?

These are typically the types of contracts player agents wish to avoid, and we haven’t seen anything quite like it since. Only the thought was the 49ers would use the excess money to re-sign a number of players set to hit the free-agent market.

Well, the 2015 offseason was a disaster for San Francisco. And not just because of retirements.

Free-agent departures, and a lack of attention given to the offensive line, turned a what-was strength into a primary 49ers weakness, as this 2015 Bleacher Report video foresaw taking place:

Maybe Baalke and the 49ers front office wanted Kaepernick to fail ever since Kap’s biggest 49ers ally, Harbaugh, was sent packing.

Let’s look back to what Jen Floyd Engel of Sporting News wrote after Kaepernick’s benching last year:

"Let’s be real, a big part of the problem is his team. They are old and untalented in all the wrong places. They inexplicably decided to self immolate and replace Jim Harbaugh with Jim Tomsula.I am sure Harbaugh was a real pain to work with or for, and yet this is a league that tolerates Greg Hardy. So you suck it up and deal. You do not dump him for Jim Light.There always was going to be a fall guy for this mess and what better person than the struggling QB with a cap-friendly exit door. The benching is just the first step to consciously uncoupling."

Or, to pour more fuel on the pro-Kaepernick-versus-anti-Kaepernick fire, let’s go back to what Tim Kawakami of the San Jose Mercury News wrote on the subject the same year:

"What began with an incredible display in 2012 coming off the bench to replace Alex Smith… under Harbaugh… and led to a Super Bowl trip and another NFC championship game appearance…Is broken asunder. And though the result was inevitable, the way the 49ers got to it, yet again, proved just how bizarre and mindlessly cryptic (and yet undeniably predictable) York, Baalke and Marathe are and will always be.Once again, when the 49ers get ready to dump somebody, they will always do it in the most awkward, self-defeating way possible.Listen, let’s figure that Kaepernick has wanted out from the time he was benched… and probably earlier, when he began to understand that York, Baalke and Marathe–or somebody close to them–were apparently dead set on leaking negative information about him.Remember his “I really hope not” answer when I asked if he believed someone in the organization was making him a scapegoat?Except: Kaepernick was a scapegoat, absolutely."

Kawakami, no stranger to front-office finger pointing, sure loved to hammer this home, didn’t he.

And while Kawakami’s extremes can cause us to groan, maybe Baalke is getting his way after all.

For what it’s worth, the 49ers inked quarterback Christian Ponder during the preseason, and the Santa Rosa Press Democrat’s Grant Cohn shared some interesting source material:

Regardless what you think of Kawakami and Cohn, you can’t think of the Kaepernick-Baalke relationship in a good light.

You just can’t.

So maybe Kaepernick should be fully justified in wanting a trade last offseason.

Injuries Come Full Circle… Almost

Remember Kaepernick taking over for a concussed quarterback Alex Smith in 2012? Kap never looked back, and Smith looked on from the sidelines.

Well, 2015 wasn’t quite like that. Kaepernick was benched because, well, he was scuffling.

Live Feed

App Trigger

Instead, those aforementioned injuries — as well as the preseason dead arm — seriously hindered any chances Kaepernick had to regain his starter crown this season. He wasn’t medically cleared until midway through minicamp, and he missed all of OTAs too.

This was vital, because it cost Kaepernick valuable time to learn Kelly’s offense.

And the whole “equal competition” during the preseason didn’t happen either because of Kaepernick’s arm fatigue.

Advantage: Gabbert.

Gabbert got the edge — he might have had it anyway — over Kaepernick because of injury. But, to be frank, Kaepernick got his edge due to Smith’s concussion.

Is it fair? Probably not. Is it football reality? Absolutely.

In case you forgot, former NFL quarterback Drew Bledsoe lost his starting job due to an injury too. The guy who replaced him? Tom Brady.

Only if Gabbert was Brady.

The Real Reason Kaepernick Lost

Everything already stated influenced Kaepernick losing the starting bid. But the No. 1 reason why it fell into place this way is simple.

Kaepernick didn’t adjust to the league after the league adjusted to him.

Kap needed an excellent running game to help set up play action and read-option passes — two areas in which he thrived. During his peak, the 49ers had some of the most intrinsic and dynamic rushing attacks in the NFL.

Putting it bluntly, Kaepernick fit well into the Niners scheme under Harbaugh. It worked. Kap thrived.

While Kawakami may have a skewed opinion, NFL Films senior editor Greg Cosell (h/t CSN Bay Area) was far more to the point:

"Obviously, I don’t know what’s in his head or how his work habits are or things of that nature. First of all, I think the 49ers with Greg Roman had the most multiple, diverse run game in the National Football League, and I think that really helped Colin Kaepernick. Now he was included in that run game because they did an awful lot with him. And that was that stretch of a couple of years where the running quarterback, with the read-option concepts, sort of took the league by storm.And then a lot of defensive coaches in the league, because they’re pretty smart, figured out how to defend that better. So you don’t see it as much now, and I think that hurt Colin Kaepernick, and you couldn’t protect him quite as much.One thing that was really evident in watching the tape was that Kaepernick did not see things clearly, so he did not advance as a quarterback in the areas that you need to advance; the mental areas of the game. He can still throw the ball really hard, he’s got a power arm, he’s still a fast runner; but I think you have to advance in the mental parts of the game both in an understanding of your own offense, and the understanding of defense.And I think he was a little stunted there up to this point."

Remember Arizona Cardinals defensive back Tyrann Mathieu’s post-Week 2 comments from last year?

Yeah, the players around the league noticed too.

Injuries and setbacks wouldn’t befall a player atone to staying a step ahead of the rest of the league. Had Kaepernick continued his upward trend from 2012 and 2013, Gabbert taking over due to Kap’s injuries merely would have been a stopgap option.

But that’s not the case.

What Now?

Let’s not end this on a ho-hum, downtrodden conclusion.

Here’s the reality: Gabbert winning out, right now, is not the end of the story.

Kaepernick lost the QB competition because he didn’t progress, mentally, in the areas he needed to. But that doesn’t mean he won’t or can’t.

Heck, maybe the Kelly elixir can work its magic. And, by some unforeseen future circumstances, the 49ers look to turn to Kaepernick once again. Maybe Gabbert isn’t on a late-blooming upward trend after all.

And the 49ers, still awash in a rebuild, decide the exploration of elongated snaps from Kaepernick this season will help them determine whether or not Kap is the best option moving forward.

In comes Kaepernick midseason and, well… it’s 2012 all over again.

Or maybe the current trend continues. All the aforementioned factors have taken their toll. Baalke and the front office have made their mark, Gabbert remains the guy no matter what and Kaepernick couldn’t do nearly enough to justify a change under center.

More from Niner Noise

• Predicting 49ers NFL Draft picks by looking at final mocks
• DraftKings NFL Draft Promo – Win $150 Guaranteed on Any $5 Bet 
• 2023 NFL Draft: EDGE Byron Young could be impact player for 49ers
• 5 low-key NFL Draft options for 49ers who are flying under the radar
• Updated 49ers salary cap space ahead of 2023 NFL Draft

Oh, the convoluted mess.

The story isn’t over, folks. Not yet at least.

Maybe Kaepernick needs a bit of luck on his side now. The chips have seemingly been stacked against him for some time, and maybe a new Chip can help work Kap back into a situation where he can thrive.

It just might not have happened on the schedule many would have hoped for.

But, for now, the quarterback battle is lost. And it shouldn’t be hard to figure out why.

Next: Gabbert vs. Kaepernick: Beyond the Numbers of 49ers QB Competiton

All statistics, records and accolades courtesy of ESPN.com, Pro-Football-Reference.com and Sports-Reference.com unless otherwise indicated.