San Francisco 49ers

Last call? Kaepernick’s 49ers fate hinges on Kelly’s

49ers vs. Seahawks: Matt Barrows' 5 players to watch

The San Francisco 49ers close their NFL season on Sunday, Jan. 1, 2016, against the Seattle Seahawks. The Sacramento Bee's Matt Barrows looks at five players whose presence or absence could have significant effect on the team as it looks ahead to
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The San Francisco 49ers close their NFL season on Sunday, Jan. 1, 2016, against the Seattle Seahawks. The Sacramento Bee's Matt Barrows looks at five players whose presence or absence could have significant effect on the team as it looks ahead to

As 2015 came to a close, Colin Kaepernick’s shoulder was in a sling, he was preparing to have two additional operations and his disenchantment with the 49ers strongly suggested he’d be elsewhere in 2017.

A year later, his relationship with the team has repaired considerably and his body even more.

“It has been a long time since I’ve felt this good,” Kaepernick said last week. “I just feel fluid on the field.”

Still, his future is just as unpredictable as it was a year ago. And entering Sunday’s finale, the biggest question surrounding Kaepernick is identical to what it was last year: Is this the last time he’ll be on the 49ers’ roster?

The answer hinges on a number of variables, including who coaches the team in 2017, Kaepernick’s controversial anthem stance and his contract for next season.

As it stands, he will earn nearly $15 million, pricey for a quarterback who’s won one game in 10 starts. Unlike in recent years, that money isn’t guaranteed, meaning the 49ers can release him at any point with little consequence to their salary cap. Furthermore, Kaepernick can make the first move by opting out of his deal, testing free agency and finding a franchise that is most committed to him.

If he did so, what kind of reception would he find? His teammates insisted throughout the season that his national anthem protest hadn’t split the locker room, and they backed up that assertion on Friday by voting Kaepernick as the winner of the Len Eshmont Award, the 49ers’ most distinguished year-end honor.

Still, his practice of kneeling during the anthem has been hugely divisive from coast to coast, and it would take a progressive owner and head coach to take on the issue. Which teams might be willing to do so? The Browns were among Kaepernick’s most ardent suitors last year and haven’t solved their quarterback issues. Or maybe it’s a wild card like the Saints or Cardinals, whose current starters at quarterback are in their late 30s.

The 49ers appear to be leaning heavily toward parting ways with general manager Trent Baalke, whose relationship with Kaepernick is cool at best.

That in itself would increase the quarterback’s chances of returning. But Kaepernick also could lose his biggest ally in the organization in Chip Kelly.

Many fans – as well as some officials inside the organization – wanted to see quarterback Christian Ponder in action as the season drew to a close. Kelly, however, has been bullish on Kaepernick throughout the season, even when Kaepernick, still recovering from surgeries, clearly was not close to full strength.

That allegiance will continue Sunday against the Seahawks. Asked if Ponder, who has been the No. 2 quarterback since Dec. 13, would play, Kelly said no.

“We’re trying to go win the football game,” he said. “So Kap will play unless he gets banged up.”

Kelly is expected to meet with CEO Jed York after the finale. York’s options are to part ways with Kelly, retain him or let an incoming general manager decide his fate.

Among the topics likely to be discussed are how open Kelly is to changes in 2017. That includes his coaching staff, something Kelly has been loath to alter as a college or NFL head coach.

Coordinator Jim O’Neil’s defense, however, ranks last in the league and already has given up a franchise record in points allowed and rushing yards allowed. If the Seattle Seahawks gain just 134 yards Sunday, San Francisco also will establish a franchise record for total yards allowed in one season.

The other major topic is the team’s future at quarterback. Ponder, Blaine Gabbert and Thaddeus Lewis are scheduled to become free agents in March. Any of them should be relatively easy to re-sign, but Kelly clearly thinks Kaepernick is the best of the bunch.

That team’s decision makers, however, are not as convinced, at least not at the amount Kaepernick is scheduled to earn in 2017.

Matt Barrows: @mattbarrows, read more about the team at sacbee.com/sf49ers.

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