Kaepernick’s success with Kelly could persuade him to stay

On paper, quarterback Colin Kaepernick‘s resurgence couldn’t have come at a better time.

When he signed his restructured contract that included a player-option for the 2017 season, Kaepernick was likely hoping to sling together the string of impressive starts he’s had as of late in the hopes of enticing new franchises in the offseason.

But those same impressive performances that were intended to play himself out of Santa Clara might also be indicative of why it would benefit both Kaepernick and the 49ers if the veteran returned for one more year.

With each game, Kaepernick has been getting better and better in Chip Kelly’s system.

After a rough two starts in which Kaepernick completed just 45.9 percent of his passes for 330 yards and two touchdowns, the quarterback has been looking more and more like the former dual-threat athlete that led the 49ers to a Super Bowl appearance.

Since then, Kaepernick has been perhaps the 49ers’ best offensive player, completing 58 percent of his passes for 1,110 yards and six touchdowns while averaging 55-yards per game on the ground.

Common sense dictates that his surge is due, in part, to him shaking off the rust from near year-long layoff after a host of injuries landed him on IR last year.

But both player and coach have indicated that there’s something more to it. Something that may bode well for Kaepernick’s future with the 49ers.

When questioned whether his improved play would tempt him to stay within Kelly’s system for another season, Kaepernick failed to give a definitive answer, but offered a cryptic look into his future with the team.

“I’m not thinking that far down the road. But, that’s very true as far as quarterbacks being in a system that they’re familiar with, they’re familiar with the coach, why they’re calling plays, they’re on the same page so when you step on that field you know exactly why your coach is calling that play, what his intent is and what you’re trying to get done.”

Kelly would later offer his own take on Kaepernick rounding into form under his watch, hinting that his progression has opened up more opportunities for both the player and the team as a whole

“He’s done a really nice job… I think as we’ve seen, there’s progression each game with him and the more he progresses, the more comfortable he is with the offense, the more you can expand what we’re doing.”

So often Kelly has spoken of seeing improvement in a 1-10 team that it’s easy to take his comments with a grain of salt. But if last Sunday’s game against Miami was an indicator, then Kelly may actually be right on the mark.

Despite earning their franchise-worst 10th straight loss, Kaepernick did just about all he could to steal a win from the streaking Miami Dolphins.

The quarterback threw for nearly 300 yards and three touchdowns while notching over 100 rushing yards. The totals marked the first time since October 2014 he’s thrown for three touchdowns, and just the second time in his career he’s rushed for over 100 yards.

Add in an improving rapport with TE Vance McDonald, and it’s easy to see why sticking around at the end of the season might be an enticing prospect to a quarterback who is playing well, but hasn’t yet managed to completely reinvigorate his career in the eyes of those outside of Santa Clara.

Even if Kaepernick does want out of the 49ers’ organization, staying with the team for just one more year and building on his late-season success could help him even more financially when he hits the open market in 2018.

But Miami’s game also showed another reason why Kaepernick might be more suited just staying in Santa Clara, albeit for factors outside of performance.

Prior to the start of the game, Kaepernick received a raucous jeer due to his controversial comments regarding a t-shirt depicting Malcolm X and deceased Cuban leader Fidel Castro.

The incident isn’t the first time that the athlete’s activism has landed him in hot water with an opposing team’s fan base, as a largely pro-military crowd during the team’s final preseason game in San Diego directed their scorn towards Kaepernick following his national anthem protests.

For a largely conservative ownership group in the NFL, any team that chooses to bring Kaepernick on-board during the height of his activism faces the risk of alienating a portion of their fan base who may not agree with his methods.

However, in the largely liberal Bay Area, Kaepernick has been praised by the majority of 49ers’ fans, the ownership and his teammates for his part in advocating for social justice.

With a growing familiarity and production in Kelly’s system, and a welcoming fan base that accepts his goal of advocating for social reform, it could pay off in more way’s than just money for Kaepernick to stay with the 49ers.

Shawn Whelchel is SFBay’s San Francisco 49ers beat writer. Follow @SFBay and @ShawnWhelchel on Twitter and at SFBay.ca for full coverage of 49ers football.