The ad campaign first shared by Nike and the quarterback Monday was a close-up of his face and a caption that read "Believe in something, even if it means sacrificing everything."
People who were infuriated over the former NFL star starting the protests for civil justice took to social media and said they were boycotting the brand.
The full video version that was released on Wednesday presents "a girl from Compton" while showing a young Serena Williams, with the controversial former NFL star heard saying, "don't just become a tennis player, become the greatest athlete - ever."
A powerful clip of Serena celebrating her 2015 US Open win is shown with Kaepernick's voice over saying "Yeah, that's more like it."
Kaepernick implores "Don't become the best basketball player on the planet, be bigger than basketball," with a clip of NBA star Lebron James opening his "I Promise" school.
"When they talk about the greatest team in the history of the sport, make sure its your team," he says as a clip is played of the US Women's National Soccer Team, the most successful international women's team ever, celebrates a victory.
Usain Bolt is shown, while Kaepernick says "Don't try to became the fastest runner in your school, or the fastest in the world, be the fastest ever."
The ad also features several athletes with disabilities, the first is a young boy without legs wrestling and winning, and a girl playing basketball in a wheelchair.
Later on in the video advertisement is the Seattle Seahawks' new draft pick, Shaquem Griffin, the first ever NFL player to have only one hand.
The campaign caused controversy in some quarters. Some even took it as far as burning their own Nike gear - and sharing images of it in flames on social media.
John Rich, one half of the country band Big & Rich, said their soundman, a former Marine, had cut off the famous swoosh logo from his socks.
Veterans organisation Vote Vets urged critics to donate their items rather than burn them.
Even President Donald Trump, who is the most vocal critic of the NFL protests that have continued beyond Kaepernick's departure from the San Francisco 49ers, took to Twitter and lashed out at Nike today.
"Just like the NFL, whose ratings have gone WAY DOWN, Nike is getting absolutely killed with anger and boycotts. I wonder if they had any idea that it would be this way? As far as the NFL is concerned, I just find it hard to watch, and always will, until they stand for the FLAG!" Trump bellowed.
However, Nike shares are up as of Thursday. Shares did fall more than 3 per cent Wednesday, but the stock is up about 28 per cent in 2018.
