49ers will keep QB Colin Kaepernick, guarantee 2016 salary

It’s unclear yet if Colin Kaepernick will be the starting quarterback for the San Francisco 49ers in 2016, but he will be in the mix. “So he’s just as excited as anybody to get out there and get going”.

Should the Niners part with Kaepernick, he would have plenty of suitors throughout the league.

Editor’s note: Matt Maiocco is in Indianapolis to cover the NFL Combine. That date marks a key fork in the road because it is when Kaepernick’s $11.9 million base salary would lock in, fully guaranteed, for the 2016 season.

“The No. 1 focus is getting him healthy”, Baalke said of Kaepernick, who’s coming off thumb, shoulder and knee surgeries. Baalke was asked whether Kaepernick would be the starter next year.

If the 49ers don’t get going, it won’t take long for Kelly, Kaepernick and Balke to be gone themselves.

In fact, leading into the combine, I’ve heard nothing much has changed between the 49ers and Kaepernick and that Kaepernick understandably remains generally distrustful of team management’s motivations.

The 49ers hired Kelly last month, three weeks after the Eagles had fired him.

Complicating matters, Kaepernick hasn’t been good the last two years. He finished with a 2-6 record, 1,615 yards, six passing touchdowns (as well as one rushing touchdown) and five interceptions.

No one seems to know how new coach Chip Kelly feels about Kaepernick, and it’s probably not going to help Kaepernick’s confidence if the 49ers are out looking for other quarterbacks, especially a quarerback like RG3, who could potentially thrive in Kelly’s system.

Baalke said the 49ers will also look at college quarterbacks such as California’s Jared Goff, North Dakota State’s Carson Wentz and Memphis’ Paxton Lynch. He said that’s why he didn’t talk to Roseman before hiring Kelly. Kaepernick’s medical history this season could have been a red flag that would have at least allowed a front office to consider moving away from the injured quarterback.

Kelly, Kaepernick and Baalke all desperately need some positive results in 2016.

Chip Kelly at his introductory press conference with the 49ers.

While the 49ers could still trade Kaepernick elsewhere, Baalke strongly indicated that wasn’t in the plans.

Trading Kaepernick might be hard.

They will not be able to wait, and sign him as a free agent. It just doesn’t make sense to not give it a chance. Yet, at his best, Kaepernick has flashed elite skill as a quarterback. You get an extra advantage of having a quarterback that can run.

As for the new start with his third coach in two years – Baalke won a power struggle with Jim Harbaugh following the 2014 season then flopped to 5-11 and last place in the NFC West last season with promoted assistant Jim Tomsula as head man – Baalke had nothing but glowing remarks about Kelly.