Kaepernick met with new 49ers head coach Kyle Shanahan and new general manager John Lynch for the first time on February 22. "I think we both agreed that under the current construct, it wasn't going to work out," Lynch said at the NFL Scouting Combine on Thursday. "But we said, 'Let's not close the door.' We had some good jokes. Once he was gone, we weren't going to have anyone. Obviously, as he hits free agency, that's something that we'll keep out eyes open and we want him to keep us in mind as well. It's something that we left that door open in a very real and positive way."
"I have a great appreciation for this organization," Kaepernick said following the 49ers' final game of the 2016 season. "Jed [York] and Paraag [Marathe], have a good relationship with them. A lot of things to think about moving forward and we'll see where this goes."
"My relationship this year was much improved from years past with Jed, Paraag," Kaepernick continued. "I think we have a great relationship now and I was excited about that. I was excited about this organization as a whole, teammates playing hard regardless of the circumstances, and coming to work every day and preparing to win regardless of what position we were put in."
Kaepernick started the 2016 season as the 49ers' backup quarterback. Recovery from three offseason surgeries and then a shoulder injury during training camp pushed him behind Blaine Gabbert in a quarterback competition to determine a starter. However, Kaepernick returned as the starter during Week 6 against the Buffalo Bills, would go on to win just one game, and finish with the second-worst Pro Football Focus grade of his career and rank 27th among all quarterbacks.
Despite the 49ers' poor play this season, Kaepernick's name dominated headlines in 2016, but not for his play on the field. The San Francisco quarterback started a protest of the traditional pregame national anthem by refusing to stand. The protest started during the preseason but was not noticed until the third exhibition game – a home matchup with the Green Bay Packers.
"People don't realize what's really going on in this country," Kaepernick said while addressing the media for the first time following that Packers game. "There are a lot of things that are going on that are unjust. People aren't being held accountable for. And that's something that needs to change. That's something that this country stands for freedom, liberty, and justice for all. And it's not happening for all right now."
As free agency quickly approaches, that protest appears to now be over. A report by ESPN on Thursday revealed that Kaepernick now plans to stand for the national anthem starting in the 2017 season.
"Kaepernick no longer wants his method of protest to detract from the positive change that he believes has been created," wrote Adam Schefter of ESPN. "He also believes the amount of national discussion on social inequality -- as well as support from other athletes nationwide, including NFL and NBA players -- affirmed the message he was trying to deliver."
Kaepernick got his first NFL start in November of 2012 following an injury to then-starter Alex Smith and went on to win five of the 49ers' final seven regular-season games before leading the team in a Super Bowl run that would fall yards shy of a sixth championship for the franchise.
This past season, Kaepernick completed 59.2-percent of his passes for 2,241 yards, 16 touchdowns, and four interceptions through 11 games.
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