Colin Kaepernick and Chip Kelly Are Getting Together Three Years Too Late

San Francisco 49ers coach Chip Kelly announced that Colin Kaepernick will take over as the team’s starting quarterback Tuesday. This type of move — made by a 1–4 team with one of the worst offenses in football — would barely register elsewhere, but in the case of the Niners and Kaepernick, it’s easily the most significant football news of the week. Ruth Bader Ginsburg isn’t talking about Jared Goff.

Kaepernick’s decision to kneel during the national anthem as a protest of police killings across the country — and the flurry of conversation that protest has created — has made him the most talked-about player in the NFL this season. And after regaining the starting quarterback job, the conversation around him will only get louder. The intrigue concerning Kaepernick extends to the football side as well, though. Not many backup quarterbacks are former playoff heroes only a few years removed from taking the game by storm, but that version of Kaepernick — and that version of his head coach — aren’t walking through that door.

I was at Candlestick Park on January 12, 2013, the day that Kaepernick — only a handful of games into his stint as Alex Smith’s replacement — took a flamethrower to the Packers defense. He rushed for a quarterback-record 181 yards, threw for 263 more, and accounted for four total touchdowns in San Francisco’s 45–31 win. Like anyone else who watched that game, I thought we were in the midst of a seismic shift. Seeing a quarterback physically outmatch an NFL defense with speed and power was new, and as read plays and mobile passers seemed poised to take over the league, Kaepernick looked like the end point in the game’s evolution.

The 49ers were an end zone incompletion to Michael Crabtree away from winning a Super Bowl that season. A year later, the same margin kept them from returning to one. In Kaepernick’s first full season as a starter, the 2013 Niners finished 12–4, powered by a bone-crushing defense and an offense that finished eighth in DVOA. Jim Harbaugh’s team boasted the league’s best offensive line, an ageless Frank Gore, and the duo of Vernon Davis and Anquan Boldin, the ideal targets for a quick-passing offense. It was Bay Area Bully Ball complete with a read-option twist. That bundle of stars with Harbaugh at the helm had the Niners looking like a playoff fixture for years to come.

Across the country, the Philadelphia Eagles were following a similar formula for offensive dominance. Chip Kelly was in his first season as the team’s head coach, and on the back of a brutally efficient running game, his up-tempo system was leaving tread marks all over opposing defenses. The 33-point firestorm Kelly’s group unleashed on Washington in the season opener felt much like Kaepernick’s playoff masterpiece against Green Bay. The revolution was being televised on Monday Night Football.

In the years that followed, the fanfare for both eventually faded, and the reason was simple. As the rest of the league evolved, neither Kelly nor Kaepernick did.

Kelly’s steadfast adherence to a handful of concepts took his system from ingenious to staid. As the 49ers offensive line and running game started to crumble, the simple, quick-decision passing game that Harbaugh had built for Kaepernick eventually fell apart. Forced to shoulder more of the burden on offense, Kaepernick’s accuracy and anticipation issues started to show. Halfway through last season, the 49ers sent him to the bench in favor of Blaine Gabbert.

Kelly’s Eagles started the 2015 season 6–8 after an internal power struggle that gave him personnel control in Philadelphia, and he was fired following a Week 16 loss to Washington. When he was hired by the 49ers two weeks later, many cited the seemingly perfect fit between Kelly and Kaepernick.

At the University of Oregon, Kelly’s teams incinerated defenses thanks in large part to his quarterbacks’ running ability. Michael Vick was already in place when Kelly arrived in Philadelphia, but in the coming years, the coach never sought out athletic options at the position, choosing Nick Foles and eventually going out of his way to trade for Sam Bradford. Not having a running threat at quarterback — even as he continued to run plays that at least appeared to be option runs — was part of the reason Kelly’s offensives had stagnated. The thought when he was hired in San Francisco was that with Kaepernick under center, we would finally see the real version of Kelly’s system.

Nope. The cold water came pouring down on that notion this summer, when Kaepernick — still recovering from surgeries to his right thumb, left knee, and left shoulder — was beaten out by Gabbert in training camp. It’s tempting to be hypnotized by memories of 2013 now that Kaepernick has the starting job, but anyone thinking this marriage is going to be as happy as it could have been three years ago is going to be disappointed.

The partnership may not work, but in some ways it does still make sense. The 49ers used play-action on 28 percent of their dropbacks in 2013 — the fifth-highest rate in the league — and finished third in passing DVOA on those throws. One of the few teams that used play-action more that year just happened to be Kelly’s Eagles. Philly led the league in that stat a season later, and even with a drop-off last year, still finished ninth. The ideal version of Kelly’s offense is always going to include a healthy amount of play fakes and simplified throws, and in that regard, it does play to Kaepernick’s strengths.

So far this year, the running-quarterback aspect of Kelly’s system has also been on full display. Gabbert had 39 rushes in the Niners’ first five games — 10 more than any other quarterback in the league. That total includes plenty of scrambles after passing plays had already broken down, but the point stands: Kelly gives athletic quarterbacks the option to carry the ball.

Those factors would make the prospect of the dominant version of Kaepernick playing in Kelly’s system an exciting one, but already Kelly has tried to downplay that notion. The player Kaepernick was against Green Bay isn’t coming back, and even if he did, the talent surrounding him still makes for one of the worst supporting casts in football.

The Niners’ most productive receiver has been Jeremy Kerley. Their offensive line is a mess outside of stalwart left tackle Joe Staley. Gabbert’s play had deteriorated to the point that there’s really nothing left to lose. At its core, that’s what this move is about.

The most significant barrier to handing Kaepernick the job prior to this week was the injury guarantees in his contract. Under his current deal, Kaepernick’s $14.5 million base salary in 2017 would become fully guaranteed if he can’t pass a physical on April 1 of next year. But multiple outlets have reported that Kaepernick’s people are working on a restructuring that would “alleviate concerns” about that number.

If that change does happen, it would leave no downside to the Niners starting Kaepernick, but now that he does have the job, it’s worth tempering expectations.

There’s a good chance that Kaepernick will be more effective than Gabbert has been, but at this point, that isn’t a high bar. This is a move more about resignation than transformation. It’s tempting to remember the league-altering personalities both Kelly and his new quarterback were just a few years ago and think that combining them can transport both back to the fall of 2013. But those days are gone. It’s still likely to be a long season for the 49ers, no matter who’s playing quarterback.