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SANTA CLARA — Kyle Shanahan is having a crisis. An existential coaching crisis. How he resolves it will define the rest of his career.

Since he came to the 49ers last year, two Shanahans have emerged: Shanahan the head coach, and Shanahan the offensive coordinator. One will overtake the other eventually — they cannot exist at the same time. Which Shanahan will win out? Which one has a future? He must choose.

Look into your heart, Kyle.

So far, the offensive coordinator has run the show to the severe detriment of the 49ers. He has made every big decision, because Shanahan trusts that side of himself. It’s the smart, confident, persuasive, successful side. The one with the answers. Shanahan the head coach has no answers yet. He lacks credentials, and his record is 7-13. He may not even last. If he fails with the 49ers, he may not get another head-coaching job.

He may be a career offensive coordinator.

Does Shanahan believe in his future as a head coach? Does he want to be a head coach?

A head coach wants to win above all else. An offensive coordinator wants to be a genius, sometimes at the expense of winning. That’s why an offensive coordinator needs a head coach to keep him in check.

Shanahan suffers from the genius syndrome. Call it Genius-itis. He got it in Atlanta when he was the offensive coordinator for the Falcons. That was 2016.

Shanahan wants to maintain his genius status. He would rather be the brilliant offensive play-caller who loses by two points and has excuses than the anonymous head coach who wins. Shanahan may not know this, but it’s the truth.

To be a genius, Shanahan has to pass the ball. No one becomes a genius by running. There’s nothing flashy or glamorous about gaining four yards on the ground. A “brilliant” offensive coordinator passes. A brilliant offensive coordinator invents scheme with intricate vocabulary.

But, a winning head coach runs. Nothing glamorous, just runs when has to. He knows an effective rushing attack will keep his defense fresh, demoralize the other team and probably win the game. That’s how football works.

Last week against the Los Angeles Chargers, Shanahan the offensive coordinator called 42 passes and just 17 runs, even though his quarterback was backup C.J. Beathard. Genius-itis. Shanahan needed to give Beathard some help, but didn’t.

What’s more, seventy percent of the 49ers’ passes included a five-man protection scheme, meaning no extra blockers. Just the five offensive lineman. Shanahan exposed Beathard to the max.

Beathard still played well. He threw for 298 yards and tossed two touchdown passes. But, he got hit 16 times and threw two interceptions, including one on the 49ers final offensive play to lose the game. They lost by two points.

On Monday, Shanahan the offensive coordinator blamed Beathard for taking those hits. Said he should have gotten rid of the ball quicker. Classic genius move by Shanahan. A brilliant offensive coordinator must protect his image at the expense of the quarterback.

But, a head coach takes the blame. Doesn’t put it on the backup quarterback.

Shanahan should have taken the blame. He’s the head coach, and he was at fault, not Beathard. Shanahan called the game as if Jimmy Garoppolo was the quarterback and made no changes to help the backup making his first start of the season. Asked way too much of him.

Shanahan the head coach should have vetoed that game plan, and explained to himself, “Look, we can’t expect to win asking our backup quarterback to drop back 42 times. We need to limit his exposure to the defense. We already lost one quarterback for the season — we can’t lose two. Plus, we have the second-ranked running game in the league and the highest-paid fullback. Plus, the Chargers defense is allowing 4.3 yards per carry. Run the ball. Take pressure off Beathard. Make a new game plan.”

Instead, the offensive coordinator got his way.

We saw that happen again near the end of the first half. The 49ers had the ball at their 25-yard line 47 seconds before halftime. They were ahead 17-14.

In that situation, a genius offensive coordinator thinks: “We can score because I’m brilliant. Let’s throw downfield and get a field goal.”

A fully mature head coach thinks: “Wait a minute. We’re winning. We don’t want the Chargers to score more points before halftime. We don’t have our starting left tackle, Joe Staley. Pass protection is an issue. We will receive the kickoff to start the third quarter. Let’s run the ball, burn time, force the Chargers to use their timeouts, go into halftime up three and start the third quarter with the ball.”

Shanahan the head coach lost that battle with himself. The 49ers passed three times, used only 17 seconds, then punted, gave up a 56-yard return and a field-goal shortly after. The Chargers tied the game before halftime.

Shanahan the offensive coordinator handed the Chargers three points. “I wish the offense didn’t put the special teams or defense in that situation, but we did,” he said on Monday, referring to the offense as “we.”

More accurate to say “I,” as in the offensive coordinator.

Shanahan the offensive coordinator continued: “It was up to our special teams not to give up a 56-yard punt return, which they did.” Notice he referred to special teams as “they,” as if he wasn’t involved.

Shanahan revealed his nature through his pronouns. This is something Jim Harbaugh thought through. The only pronoun he used was “we.”

And Shanahan revealed his nature when he recklessly wasted two timeouts in the second half challenging plays he shouldn’t have challenged. He lost both challenges, meaning he lost two timeouts he needed and didn’t have at the end. Ultimate genius-itis.

A head coach doesn’t risk losing timeouts. He knows the team with more of them has an advantage at the end of a close game. He overrules the offensive coordinator.

Overrule your inner offensive coordinator, Kyle. He had his time. You’re a head coach now. Be one.

Grant Cohn covers the 49ers and Bay Area sports for The Press Democrat and Pressdemocrat.com in Santa Rosa. You can reach him at grantcohn@gmail.com.

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