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That Kaepernick struggled is not a surprise. Throwing for 600 yards, four touchdowns, and no interceptions against the New York Giants and Baltimore Ravens, two of the five worst pass defenses in the NFL, is a lot easier than doing it against the Seahawks' Legion of Boom secondary.
More importantly, for Kaepernick and the 49ers, struggling has become the norm and it is going to cost him millions.
Prior to the 2014 season, the 49ers raised a lot of eyebrows when they signed their young, supposedly franchise quarterback to what was being called a "record" 7-year, $126 million contract with $61 million guaranteed. But this is the NFL and to them, "guaranteed" doesn't mean what it means to the rest of English-speaking world.
Thanks to some fancy wording ($12 million in unlikely bonuses were built into the deal as "de-escalators"), and with most of the $61 million only being guaranteed against injury, the $49ers had a contract that was extremely team friendly and one they could easily get out of at any time. Every off-season during the contract, the 49ers are free to release Kaepernick and they would never have to pay him another dime.
If this was baseball, we would have never called it a 7-year, $126 million contract. Rather, we would have called it a 1-year, $13.1 million contract with six option years.
But that doesn't sound as sexy, does it?
Fast forward to March, 2016. Kaepernick's 2016 salary guarantees on April 1, 2016. With bonuses, he will earn $14.3 million next year. If the 49ers cut him, they don't owe him anything and they would save $9.4 million against the salary cap.
At this point, it is worth speculating whether this is Kaepernick's final year with the 49ers, and on a contract that still has $100 million left on it.
Kaepernick is not only a player who has not developed into a franchise quarterback, he is actually regressing. How often he throws a touchdown has declined two straight years and his frequency of interceptions has risen every year.
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Also, if we look at his adjusted yards per attempt (yards per attempt, adjusted for interceptions), a good indicator of a quarterback's production while throwing the ball, Kaepernick's number has fallen each year. He actually led the league in this category in 2012. So far this season, he is 18th.
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It will be difficult to justify paying Kaepernick $14.3 million next season for this type of production. In other words, there is a good chance this is Kaepernick's last season with the 49ers.
If Kaepernick is let go in the off-season, he would have earned $25.9 million in two years since signing his deal. That means he would never see $100.1 million of his so-called $126 million contract.
That's a pretty hefty price to pay.