What should Chip Kelly and the 49ers do with Colin Kaepernick?

On Thursday, history repeated itself. The 49ers hired a wildly successful former Pac12 head coach with a headstrong approach to running a football team. It paid immediate dividends the last time, when the Niners hired Jim Harbaugh away from Stanford in 2011. If they want similar instantaneous results with Chip Kelly, the first question they’ll have to answer is whether a key player from Harbaugh’s tenure, Colin Kaepernick, is still the answer at quarterback.

It’s not easy to find a franchise quarterback, but the 49ers figured they had one when they signed Kaepernick to a six-year, $114 million contract in 2014. Since then, Kaepernick’s play fell off and the relationship between the team and its quarterback got strained, kind of a theme with the 49ers lately.

The first and most important question to ask is whether the fences can be mended between Kaepernick and the team. Things got so bad it’s been widely assumed that the 49ers would either trade him or release him this spring before his 2016 salary becomes fully guaranteed on April 1. However, Ian Rapoport reported Thursday afternoon, following the Kelly news, that general manager Trent Baalke had gone to Kaepernick to make peace before the season ended.

Whether the move works remains to be seen. Before we get into the back and forth of whether Kaepernick and Kelly are a good match, let’s take a quick look at the salary cap situation with Kaepernick’s contract, since that’s been pointed to as a concern for if the team can keep him.

Kaepernick’s deal came with $61 million in guaranteed money, but it was one of those deals where the team has a series of easy outs built into it. He’s scheduled to count $15.89 million against the cap this year. Cutting him would leave less than half of that on the books as dead money. His cap hit takes a jump next season to $19.36 million, and it goes up from there to $23.4 million in 2020, the last year of his deal.

That’s a lot of cap space, but that’s the one thing the 49ers have plenty of this season. Baalke has more than $44 million to work with, according to Spotrac, the fourth-most of any team. He also has a lot of needs to fill, but Kaepernick’s contract isn’t any more odious than the typical franchise quarterback contract, especially when the cap is increasing by about $10 million every year.

The question is, can he play up to that kind of deal again?

By James Brady

Colin Kaepernick didn’t find himself benched in favor of Blaine Gabbert, of all people, because Jim Tomsula was his head coach and Geep Chryst was his offensive coordinator. Kaepernick was one of Chryst’s biggest supporters, and the 2011 second-round pick was already in a steep decline when Jim Harbaugh and Greg Roman were still calling the shots.

In 2014, Kaepernick completed 60.5 percent of his passes with 19 touchdowns and 10 interceptions, but he also had three fumbles and some of his passes were just egregiously bad.

The most concerning thing about Kaepernick wasn’t that he threw a lot of interceptions, but that he was making mistakes at a very basic mechanical level. He wasn’t going through his reads on the field, he wasn’t comfortable in the pocket and he often missed wide open receivers. The offense didn’t lose games outright, but it always felt like it was just along for the ride. Kaepernick wasn’t dangerous.

This past season, he was even less dangerous. He averaged 6.62 yards per pass attempt and threw for under 200 yards five times before he was benched. He threw for over 200 yards just three times last season. He finished five games without throwing a touchdown.

Kelly’s offense and what he looks for in a quarterback certainly matches up with what Kaepernick can do on paper. It’s a convenient fit and we won’t know for awhile how much the potential to salvage the relationship factored into Kelly’s hire. But it’s not as simple as plugging Kaepernick in and telling him to use his legs to make things happen and use his big arm to hit Torrey Smith deep on every play.

Kelly will have to re-teach Kaepernick how to play quarterback in the NFL, and it won’t be an easy task. Kelly is probably the only coach the 49ers could have hired to even make the notion of Kaepernick returning to the 49ers in 2016 anything more than completely ridiculous.

By Danny Kelly

Colin Kaepernick regressed badly over the past two seasons as the 49ers attempted to make him more of a pocket passer and traditional drop-back quarterback. His accuracy dipped, his YPA dropped and teams began to say that he had become very predictable in his reads. It didn’t help that the Niners’ run game was suffering and the protection up front got considerably worse. The result was that a normally confident and aggressive passer became frenetic and unsure behind the line.

The thought that Chip Kelly could help massage some of those issues out is an interesting one. By giving him defined reads and helping him get the ball out quickly and decisively in the Chip Kelly “packaged play” offense, Kelly could help to mend some of the confidence issues that seemed to plague Kaepernick before his benching. Accuracy could take a jump. Turnovers could drop. Getting Kaep into a fast-paced Pistol or shotgun offense could help him regain some of that rhythm that has been missing from his game.

Kaepernick is obviously very dangerous with his legs, so incorporating him into the read option game would be an great fit. When you have a quarterback that threatens to take a run to the house like Kaepernick can, defenses have to plan their game differently, and the math changes. This could, in turn, help San Francisco get their run game back on track, particularly once Carlos Hyde gets healthy.

Overall, it’s very intriguing in theory. Minus the running aspect of it all, I had pretty high hopes for what Sam Bradford could do to resurrect his career in Philly under Kelly. If you look at the second-half splits, he was definitely trending in the right direction.

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