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Shanahan has been five steps ahead of his opponent all season

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Kyle Shanahan is playing 5th dimensional chess

Carolina Panthers v San Francisco 49ers Photo by Lachlan Cunningham/Getty Images

Kyle Shanahan has gotten a lot of praise for shrewd play-calling this year, which is well deserved. But his genius — yeah, I said it — goes much deeper than that.

He doesn’t just collect plays like Magic the Gathering cards and deploy them against defenses. Great play-calling understands why a play was developed — what defensive strategy it was created to exploit, which tendency it counters — and orchestrates the defense’s reactions.

On the latest Better Rivals podcast, Oscar Aparicio pointed out another deep nuance: knowing the keys that defenses react to, and falsifying them by making the players keyed on “lie” with their movements.

Many people have said that the Niners D and run game is amazing this year, but their passing offense is meh and might get exposed when it’s needed against tougher opposition. I beg to differ.

Obviously, the 49ers have been emphasizing the run. Why? Because they can.

Any team in the league would run for 232 yards in a game if they could even though their three best blockers were out injured. You control the clock, prevent interceptions and strip-sacks, and frustrate the trend of the league, which has been to focus on the passing game with a lot of nickel and dime packages.

Few teams can do that, though, because they optimize their OL for pass protection and only have one good running back (who wouldn’t stay healthy if they did). The Niners RB by committee and OL depth makes the strategy possible.

But scoring 51 points with only 175 yards of passing has another advantage. I think that Kyle Shanahan is hiding his light under a bushel basket, passing as little as possible to hide his twists from the prying eyes of defensive quality control assistants on upcoming opponents. Film-proofing his scheme by not giving them any film to scour, and carefully choosing what he puts on tape to mislead them.

Here is the statistic that stunned me:

Can that be right? I had to verify, but it checks out. Garoppolo has not thrown two TDs to any target. And you will never convince me that this is an accident.

Four of the people catching tuddies touchdowns aren’t even wide receivers: George Kittle, Raheem Mostert, Tevin Coleman, and Matt Breida. In fact, 4th string RB Jeff Wilson, Jr. and 5th string WR Kendrick Bourne are the only backs who haven’t caught touchdowns this year, and they probably will later.

So let’s say you’re a defensive coordinator scheming up a game plan. Who should your best CB (say, Stephon Gilmore) cover? Gilmore, like the RamsJalen Ramsey, wants to play the offense’s best receiver — but who is that?

George Kittle? Emmanuel Sanders, now? Whatever. Shanahan can send that target deep, on the far side of the field, and attack the rest of the turf with four other targets, safely away from him because every single skill player on the Niners is a good receiver.

Of course, there are talent differences between receiving targets. I think Shanahan is deliberately spreading it around, so there is little or nothing for film junkies to find, no matter how many hours they go over tapes.

He also has a bit of lemonade coming from injury lemons. (That’s a horrible metaphor, I’m sorry.) The team has de-emphasized deep passes because two backup offensive tackles are protecting Garoppolo, so it would be foolish to give the long plays the time they need to develop. That hides the attack even more.

The scheme’s crucial fullback, Kyle Juszczyk, has also been out injured. He is both a crucial 3rd down pass protector and a big-play threat in his own right, who would probably be the tenth TD recipient by now if he had stayed healthy.

So fret not, Niners faithful. The passing game isn’t weak. It’s waiting.