Will 49ers pull an RG3-type shutdown on Colin Kaepernick?

Colin Kaepernick

John Hefti-USA TODAY Sports

Colin Kaepernick returned to practice Wednesday but didn’t appear any closer to providing answers to the questions surrounding the San Francisco 49ers’ QB situation.

Kaepernick, who’s been sidelined with what the team called "arm fatigue", suited up for Wednesday’s practice and scrimmage with the Denver Broncos, but didn’t take part in any passing drills. GM Trent Baalke addressed the report that Kaepernick has a dead arm and while he refused to make that "assumption," he didn’t deny it, either.

Either way, it’s becoming increasingly apparent that Blaine Gabbert will the the Week 1 starter, Tim Kawakami of the San Jose Mercury News writes. Baalke, he suggests, would be in favor of that. 

It’s also looking less likely that Kaepernick will return to the form that earned him a $114 million contract — at least with San Francisco. And the big bucks involved may dictate what happens next — and what’s happened to this point.

Kaepernick scrapped a potential trade to the Broncos earlier this offseason because he refused to take a pay cut, and the 49ers refused to pay $5 million of his $12 million salary, Kawakami reports.

“We couldn’t hand him the starting job. He was going to be in a battle for the starting job," John Elway told USA Today earlier this week. "We had to protect ourselves if he wasn’t the starter, and that’s where we went and stayed there. He made the decisions, the Niners made the decisions and it ended up where it is right now.”

The 49ers can save $2 million in weekly roster bonues if Kaepernick is not active, Kawakami reports. And his $14.5 million salary for 2017 is guaranteed only if he suffers a serious injury, which the 49ers could prevent by keeping him off the field, as the Washington Redskins did with Robert Griffin III last year.

But Baalke did deny the 49ers would hold him out over financial factors.

"No facts," Baalke told reporters, via the Sacramento Bee. "… Like we maintained all along, Kap’s going to be given every opportunity, just as Blaine is, just as Christian (Ponder) is, just as Thad (Lewis) was. They’re given every opportunity to earn that role."

However, our own eyes tell us otherwise, Mark W. Sanchez of the New York Post writes.

Instead, as Gabbert eats up every first-team rep, Kaepernick is literally going through the motions. Wednesday, during a joint practice with the Broncos, Kaepernick consistently dropped back during drills, but didn’t throw the ball. The 28-year-old racked up mental reps for the fifth straight time — four practices, one game — as all signs point to a phasing-out that would get the 49ers out from under his contract.

The whole thing is frustrating to 49ers fans, who are enticed by the prospect of a healthy, dynamic Kaepernick running Chip Kelly’s offense.

It also has to be frustrating to Kelly, who’s stuck with a mediocre Gabbert for now. But if Kaepernick gets healthy and Gabbert fares no better, Kelly may be determined to turn Kaepernick loose, Kawakami writes.

“The head coach is going to decide who the starting quarterback is for the San Francisco 49ers,” Baalke said Wednesday.

For now, all Wednesday served as is a reminder that Kaepernick remains the 49ers’ problem and not the Broncos’.