Harbaugh is now the head football coach at the University of Michigan. He coached Kaepernick for four years in San Francisco. The two paired up for a championship appearance in 2013, falling short to John Harbaugh's Baltimore Ravens 34-31 in Super Bowl XLVII.
Jim Harbaugh left the 49ers for the Wolverines following an 8-8 campaign in 2014. Kaepernick ascended as a team leader. During the 2016 season he became more than just a team representative. The quarterback took a stand for social justice, or more appropriately, a knee.
Kaepernick started an NFL trend by taking a knee during the pre-game national anthem before every contest. He did so to bring attention to social and racial injustice and police brutality. Multitudes of players from other football franchises joined his effort.
"Colin Kaepernick was alone in his early protests last year when he boldly and courageously confronted perceived inequalities in our social-justice system by refusing to stand for the national anthem," Harbaugh wrote for Time. "At times in our nation's history, we have been all too quick to judge and oppose our fellow Americans for exercising their First Amendment right to address things they believe unjust."
Kaepernick was never fined for his pregame ritual, but he was the target of vitriol from many critics.
His former coach said his act should be celebrated.
"Rather than besmirch their character, we must celebrate their act," Harbaugh wrote. "For we cannot pioneer and invent if we are fearful of deviating from the norm, damaging our public perception or -- most important -- harming our own personal interests."
Kaepernick is now saying he will stand for the anthem during the 2017 season, but the free agent has yet to sign with a new team. He opted out of his 49ers contract in March.
Harbaugh added that he thanks Kaepernick for his contributions to football and applauds his courage in demonstrating his right to free speech.
"How lucky for us all and for our country to have among our citizens someone as remarkable as Colin Kaepernick," Harbaugh wrote.
The seventh-year quarterback also made noise in November when he talked about the "good things" done by former Cuban communist leader Fidel Castro.
"What I said was I agree in the investment in education," Kaepernick said in November after the 49ers lost to the Miami Dolphins in Davie, Fla. "I also agree in the investment of free universal healthcare. As well as the involvement in him helping end apartheid in South Africa. I would hope that everybody agrees that those things are good things. Trying to push the false narrative that I was a supporter of the oppressive things that he did, it's just not true."
Despite all of the outside noise and criticism, another of Kaepernick's former coaches said he didn't cause any distractions for the team.
"There was zero distraction," Chip Kelly told Sports Illustrated in March. "He met with the team immediately after [his first protest]. He met with the other team leaders. He explained his position and where he was coming from. And literally, that was it."
Kelly coached Kaepernick for just one season before being fired in January.
"Colin was focused on football. He was all about the team and trying to help us win," Kelly said.
Kaepernick won the Len Eshmont Award last season, given to the 49ers player who is the most courageous and inspirational on the team.
Just because he hasn't agreed to terms with a new franchise doesn't mean Kaepernick's offseason has been lost. In March, the quarterback teamed up with actor Ben Stiller and Turkish Airlines, championing the Love Army for Somalia effort. The project resulted in the airliner agreeing to carry food and supplies to assist the people of Somalia during its famine.
His evolution from a dual-threat quarterback to one of the league's most polarizing figures won't be forgotten by front offices, but Kaepernick's former teammates remain mystified about why he hasn't signed with another team this offseason.
"I've seen some quarterbacks who got signed that, in my opinion, Kap is way better than," 49ers running back Carlos Hyde told CSN Bay Area in April, "But, you know, I'm not a GM. I'm not a head coach. So that's out of my league."
Reports have surfaced attempting to explain why teams have yet to sign the quarterback. The reported reasons for his lengthy limbo range from a high asking price to concerns about his vegan diet.
Kaepernick, 29, went 12-4 in 2013, his first full season as a starting quarterback. After an 8-8 campaign in 2014, he has slipped to 3-16 as a starter in the last two seasons. In 2016, he completed 59.2 percent of his passes for 2,241 yards, 16 touchdowns, and four interceptions. He also ran for 468 yards and two touchdowns.
Organized team activities begin between late May and mid-June, depending on the team, following next week's 2017 NFL Draft. The first preseason game is the Aug. 3 Hall of Fame Game in Canton, Ohio.