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Colin Kaepernick will be 49ers' backup QB, but intrigue rests with what happens next

SANTA CLARA, Calif. -- On Saturday, San Francisco 49ers coach Chip Kelly announced what was obvious to anyone who had been paying attention: Blaine Gabbert is the 49ers' starting quarterback. Whether that's a permanent condition remains to be seen.

Kelly also said that Colin Kaepernick is the No. 2 quarterback with Christian Ponder occupying the third spot. While Kelly prefers to keep three quarterbacks, he also has the same plan for game days that the rest of the league does, which is to say only the top two quarterbacks will be active.

“Right now, I have met with our quarterbacks, Blaine is No. 1 and he’ll start versus the Rams and Kap is No. 2,” Kelly said. “We’ll only have two guys up [at quarterback] on game day.”

Based on that response, it's fair to assume those two guys will be Gabbert and Kaepernick for the time being. That wouldn't mean much were it not for some financial reasons that lurk this season and beyond.

The Niners were already on the hook for Kaepernick's $12.3 million salary this season but he gets a $125,000 bonus for each game he's on the active 46-man roster, which could add another $2 million to his salary. Taking it a step further, the 49ers would owe Kaepernick a guaranteed $14.5 million base salary in 2017 if he were to play and suffer an injury that prevented him from passing a physical by April 1 of next year.

That last caveat has left some outside observers wondering whether the 49ers would take the same approach Washington did with Robert Griffin III last year when the Redskins kept Griffin on the roster but never played him to keep him out of harm's way. Griffin was released after the season.

For now, that doesn't appear to be the plan for Kaepernick, whom Kelly has maintained all along is one of the two best quarterbacks on the roster. And Kaepernick's decision to sit or kneel during the national anthem to protest racial oppression in the United States will also have no bearing on Kaepernick's status.

“When he’s here at 4900 [Marie P. DeBartolo Way], he’s all about football and all about work and that’s what I’ve seen since he’s been here,” Kelly said. “He continues to display that every day he’s in this building.

“How he’s handled himself and how he’s been with us, I have no issues with Kap at all.”

While the Niners seem prepared to go with Kaepernick as the backup, the other side of the coin is whether he'll have a chance to unseat Gabbert as the starter. It's a proposition that didn't seem out of the question at the outset of training camp, even if Kaepernick was playing from behind.

Back in the spring as Kaepernick recovered from shoulder, thumb and knee injuries, Gabbert got the first bite of the apple in Kelly's fast-break offense. Kaepernick was left taking mental reps while Gabbert did the real thing.

As training camp opened, Kelly wanted to let both players get equal reps with the first team and they did for a handful of practices before Kaepernick's right shoulder could no longer bear the burden of throwing between 86 and 102 passes per practice. It was too much stress on a shoulder that hadn't been asked to do so much for months. It cost Kaepernick two preseason games and, perhaps more importantly, joint practice sessions with the Denver Broncos and Houston Texans.

In the end, the lack of cooperation from Kaepernick's body might not have been the worst thing for him. He can now work on regaining the weight he lost in his absence, continue to take real reps that allow him to get a better handle on Kelly's offense and build on what he was able to do in the preseason finale against San Diego.

Meanwhile, Gabbert will have the unenviable task of trying to solve a schedule that includes defenses like Los Angeles, Carolina, Seattle and Arizona in four of the first five weeks. All of that for a quarterback who has the worst QBR of regular starters in the NFL since he came into the league in 2011 and is surrounded by one of the least-accomplished receiving corps in the NFL.

And one more thing: In three years as a head coach in the NFL, Kelly has never had a quarterback start all 16 games, which is partially why the 49ers kept Ponder.

“I think you need to have three [quarterbacks] in this league with the injury rate of quarterbacks,” Kelly said. “I have never been comfortable with keeping two. I think you need to have three and I think Christian’s performance, coming in on a short week against Denver and how he played there and the performance of how he played last Thursday night against San Diego gave him the opportunity to earn the No. 3 spot.”

One way or another, it's entirely possible the Niners will have to make another decision on whether or not to play Kaepernick this season. So while Kelly's unsurprising announcement that Gabbert is the starter ended the competition, there's still plenty of quarterback intrigue to watch as the regular season begins.