In fact, the deal was terribly lopsided — in the 49ers’ favor. Although Kaepernick’s annual salary was in the range of what top quarterbacks were getting — he was guaranteed almost $13 million in 2014 — there was clause after clause that benefited the team. Most marquee players have contracts calling for the team to pay for a disability policy in case of a career-ending injury; Kaepernick’s contract called for him to pony up for a $20 million policy that would be paid to the 49ers. If Kaepernick didn’t suit up for a game, it would cost him $250,000 — far more than most other players. There was an annual $2 million salary “de-escalator” unless he was named to the All-Pro first or second team or won the N.F.C. title game. And on and on.

And that $61 million in guaranteed money? It was a mirage. Much of that money was tied to an “injury guarantee” clause; it said that if Kaepernick was seriously injured in one season, and remained injured as of April 1 the next year, he would have to be paid his entire salary for that second year. That was certainly more protection than players had gotten in the past, but it was hardly a $61 million guarantee.

Why, you might be wondering, don’t football players have the kind of financial protection against injury that baseball and basketball players have? The obvious answer is that the owners are fiercely opposed to it. Serious injuries are far more common in football than in baseball and basketball. Paying players who are hurt for more than one season would be expensive. In addition, the N.F.L. operates under a “hard” salary cap. Using part of the cap to pay injured players would make it difficult to field a roster of talented players.

And while marquee players operate from a position of strength, the average player doesn’t have much leverage. The typical length of an N.F.L. career is less than four years, and most football players are surprisingly fungible. So few of them are willing to hold out for contract guarantees. They know what happened in 1987 when the players went on strike only to see the owners hire replacement players — and break the strike in less than a month. More than athletes in other sports, football players fear for their jobs. And the owners know it.

Which brings us back to Kaepernick. Observers of the 49ers will tell you that by the time he was benched in November 2015, the relationship between Kaepernick and the team’s management had soured. Kaepernick felt he was being blamed for the team’s decline — even though the coach who had transformed the team, Jim Harbaugh, had departed and the talent surrounding Kaepernick wasn’t nearly what it had been just a few years earlier. The front office felt that his skills had declined so much — he was the league’s 30th-ranked passer — that he no longer merited an elite quarterback’s pay.

In late November, Kaepernick had shoulder surgery (which, because of his contract, cost him money because he was no longer suiting up for games). Two months later, he had operations on a thumb and a knee. And a month after that, he demanded a trade.

The 49ers shopped him around, and though a few teams were interested, they all wanted Kaepernick to take a pay cut, which he refused to do.