In one scene of the season 20 premiere, a black schoolgirl is shown in a gym as commentators obsess over whether or not she will be on her feet for the anthem.
The commentators say: "This week with athletes all over the country sitting down for the national anthem, the question on everyone's mind is: 'What is this little girl going to do?'"
It then cuts to two audience members - one of whom has a bet on her actions.
In another part of the show, a cartoon version of Kaepernick himself appears.
As the anthem plays he stands, rests on one knee, swaps knees and then leans on both at once.
The confusion over what to do is mirrored in the stadium as members of the crowd stand and sit at different times.
American Kaepernick recently said he doesn't want to protest forever - but will if things don't change.
He said: "I don't want to kneel forever. I want these things to change.
"I do know it will be a process, and it is not something that will change overnight.
"But I think there are some major changes that we can make that are very reasonable."
Kaepernick has been criticised in some corners of the NFL and supported in others. Three Tennessee Titans players raised their right fists in the air after the national anthem in their last game to raise awareness about inequality in American society.
"I don't want it to be taken as something that was us trying to separate people," defensive linesman Jason McCourty said.
"It was more trying to bring everyone together in solidarity trying to come up with a situation to better our country. We love it, but that doesn't mean that we don't have room for improvement."
Denver Broncos linebacker Brandon Marshall took a knee during the NFL season opener last week in a show of solidarity with Kaepernick, while 49er Eric Reid followed his backup quarterback's lead by doing the same in San Francisco's first match against the LA Rams.
