49ers GM says Colin Kaepernick ‘absolutely’ will return in 2016

Kaepernick’s $12 million salary becomes guaranteed on April 1. Baalke said the expectation was that Kaepernick and Gabbert would compete for starting job. Adding a linebacker or star defensive back could be the route for San Francisco if Kaepernick is retained for the 2016 season.

The 49ers brass is expected to meet with Kaepernick’s representatives this week in combine.

Baalke first met Kelly when the coach was at the University of OR, and they’ve had a positive relationship ever since, Baalke said.

“I’ve had a couple brief conversations with him”, Baalke said. “The main focus right now is getting him healthy”.

“I expect him to come back”, Baalke said in a lounge area of Lucas Oil Stadium, site of combine workouts that began Wednesday.

“We’ve got two guys who have gone into games and proven they can play”, Baalke said at the NFL Scouting Combine in Indianapolis on Wednesday.

Even Kaepernick does want to leave the 49ers, where would he go?

But the 49ers probably don’t want to pay Kaepernick his full 2016 salary; Kelly has seemed just as intrigued by Gabbert, who is onboard for only $2 million. The 49ers keeping Kaepernick could also potentially take them out of play for a quarterback at No. 7, which could mean there will be one available for the Eagles at No. 13.

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

“I always say there’s perception and there’s reality”, Baalke said. Leading up to his dismissal, reports surfaced that Kelly had lost control of the locker room, and questions over his relationships with the team grew louder when owner Jeffrey Lurie said he wanted a coach who would “open his heart to his players”. Numerous reports suggested Kaepernick was being set up to fail so that the team would have no problem moving on from him following what turned out to be a disastrous 2015 season.

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.