Lost in all the drama surrounding San Francisco 49ers head coach Jim Harbaugh is the fact that the team’s franchise quarterback Colin Kaepernick and his future in Northern California may very well be tied to what happens with Harbaugh at season’s end.

The dynamics at play here aren’t unfamiliar.

Kaepernick was Harbaugh’s hand-picked selection in the second round of the 2011 NFL draft. In fact, general manager Trent Baalke was leaning in Andy Dalton’s direction when the 49ers were in discussions to trade up for one of the two in the second round of that particular draft.

Since the 49ers selected Kaepernick out of Nevada-Reno, the process that took him from wide-eyed backup to starting in the Super Bowl and then to point where he’s facing unjust criticism today isn’t something we can just gloss over.

Harbaugh made the decision to go with Kaepernick over Alex Smith midway through the 2012 campaign. He did this despite the fact that Smith had led the 49ers to the NFC Championship game the season prior. He did this despite the fact that some viewed Kaepernick as being unprepared to take over the starting role for a Super Bowl contender. Going from a veteran to a young option at the all-important quarterback position is something non-contending teams normally mull over. It’s definitely rare to see an upper-echelon team go through that change in the middle of the season.

From that point on, Kaepernick has been seen as Harbaugh’s project. The two have built a strong relationship with a backdrop that consists of neither having a good relationship with the mainstream media in the Bay Area. Even today, Harbaugh has found it worth his time to defend Kaepernick from the criticism he has received as it relates to a perceived standoffish attitude with the media.

However, the built-in dynamic around 49ers headquarters in Santa Clara is the larger story here.

If Kaepernick is indeed seen as Harbaugh’s guy, what happens to the former if the latter departs the 49ers (as expected) following the 2014 season? Would Trent Baalke and another head coach view Kaepernick as an extention of the Harbaugh era or would they give him a fresh start?

On the field, Kaepernick has the look of a franchise signal caller that’s stuck in neutral. He’s improved in certain aspect of the game such as finding his secondary reads and showing better pocket awareness. But as the 49ers offense continues to slide back, Kaepernick’s game has been placed further under the microscope. He struggles with intermediate accuracy, doesn’t put the necessary touch on the ball and seems to lock in on one receiver at times. These are traits that scouts knocked Kaepernick on when he entered the 2012 NFL draft. They are also traits that seem to be stuck in neutral under Harbaugh.

With that said, Kaepernick’s on-field success is undeniable. He has put up 55 career touchdowns and just 19 interceptions for a solid 91.6 quarterback rating. The athletic signal caller is also completing over 60 percent of his passes and averages a solid 7.7 yards per attempt.

This has translated to a career 24-11 record as a starting quarterback for the 49ers.

These are numbers you simply cannot discount.

But they are also numbers that a potential new head coach may not take into account when all is said and done. As we have seen numerous times in the past, coaches like to have their own quarterback. Their own project. This was obviously the case when Harbaugh “benched” Smith in favor of Kaepernick.

With a lot potentially invested in Kaepernick long term, there will undoubtedly be a conversation between Baalke and a new coach about his future should Harbaugh move on following this season.

The six-year, $114 million extension Kaepernick signed with San Francisco called for $61 million in guarantees. When that extension was announced, many jumped to conclusion that the 49ers had placed too much trust in the young quarterback. But when we looked into it further in the days following the announcement of the extension, that obviously wasn’t the case. San Francisco can get out of the deal on a yearly basis prior to April 1 without ANY long-term salary cap ramifications.

And that’s where this story gets going.

If Harbaugh were to leave, the 49ers could technically move on from Kaepernick following this season and not have to worry about being placed behind the proverbial eight-ball as it relates to the salary cap. However unlikely that might be, it’s something to consider based on the factors we listed above.

It’s also something that has to be weighing on Kaepernick’s shoulders at this point. He’s worked hard to build a life and foundation in the Northern California region. If his future in San Francisco is indeed tied with Harbaugh, there has to be some concern that the 49ers might not be all in moving forward.

That concern was relayed to me by someone close to the situation in Santa Clara recently. The dialogue of that conversation was as follows. Speaking on Harbaugh’s situation, the thought process here was that it makes some wonder about Kaepernick’s future in San Francisco. And while he’d love to retire a 49er, he’s “Jim’s guy, not Trent’s.”

So as the NFL prepares for the final quarter of the season and rambling persists as it relates to Harbaugh’s future in San Francisco, it’s important to note that there is more on the line here. Others will be impacted by what happens between the head coach and his current franchise. None more so than the individual Harbaugh himself went out on a limb for. And someone who hs rewards Harbaugh for doing just that.

Colin Kaepernick.

Photo: USA Today