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Win or lose Saturday, Harbaugh made right decision with Kaepernick

Photo: Stacy Revere/Stringer/Getty Images

Colin Kaepernick, who boasts a 98.3 QB rating, threw 10 touchdown passes and just three interceptions during the regular season.

You may not realize this yet, but you will soon: The storyline for this weekend's 49ers">49ers-Packers playoff game has already been written. It's about 49ers quarterback Colin Kaepernick.

If the 49ers win, then coach Jim Harbaugh was brilliant for making Kaepernick his starter even after Alex Smith was cleared to play. If the 49ers lose, Harbaugh was wrong. This is the obvious angle for anybody who analyzes the game. I can see it from 2,000 miles and three days away.

I understand this completely. But I'm going to reach a verdict before the trial. Harbaugh absolutely made the right decision to start Kaepernick.

The 49ers might lose to Green Bay. Aaron Rodgers might outplay Kaepernick. (That one will probably happen -- Rodgers is the best player in the league.) But the 49ers have their quarterback, for this year and the next decade. And they only know that for sure because Harbaugh made the incredibly bold decision to bench Alex Smith.

"He is a man of just the right amount of words," Harbaugh told me last week, and this is not what people usually talk about when they discuss Kaepernick. They talk about his athleticism, his explosiveness, his ability to turn a 6-yard sack into a 40-yard gain.

Still: Just the right amount of words. Harbaugh meant that Kaepernick doesn't blend into the wallpaper, but he also doesn't go overboard trying to show everybody he is a leader.

Kaepernick has a presence and self-confidence that can't really be coached, and can't even be detected until you see him in the fire of an NFL game. Quarterback is not like other positions. A middle linebacker or left guard who dominates practice will probably be great in games. But quarterbacks have to make so many decisions under duress, and face so much scrutiny, that you need to see them in a game to understand how good they are. If the pressure forces a supremely talented quarterback into five terrible decisions per game, he is a bad quarterback, no matter how tight his spirals are.

There is a great stat that shows how well Kaepernick has handled the gig. I'll get to it in a minute. First, let's look at how Harbaugh and Kaepernick arrived at the week of Nov. 25, when Smith returned from a concussion and Harbaugh stuck with Kaepernick, who had played one full game, a dominant performance against the Bears.

Back when Harbaugh coached Stanford, his star quarterback, Andrew Luck, attended the Manning Passing Academy. When Luck returned to Palo Alto, Harbaugh quizzed him on the other quarterbacks at the camp. Luck told his coach that he really hit it off with the kid from Nevada, Colin Kaepernick. Since Harbaugh views Luck as the epitome of all that is right with humanity -- he has called him "perfect" -- the endorsement stuck with him.

By the 2011 draft, Harbaugh was a rookie NFL head coach and Kaepernick was a talented prospect, but there were serious questions about how he would do in the NFL. He had thrived in the pistol offense at Nevada, but hey, that was Nevada, and even though it was only two seasons ago, the NFL was a different league. Nevada's offensive scheme seemed a long way from the NFL. Harbaugh started digging.

Harbaugh himself became a longtime NFL quarterback mostly because of will -- he was considered the second-best high school quarterback prospect in his own area of Northern California and faced questions about his physical ability all the way until he retired. He succeeded because he damn well wasn't going to let himself fail.

Kaepernick seemed different from Harbaugh -- a 6-4, 230-pounder who could break 50-yard runs and rifle passes across the field. But Harbaugh discovered that Kaepernick had a lot of the same qualities that Harbaugh had as a player. He was lightly recruited to Nevada. The Chicago Cubs had offered him a generous amount of money just to play some minor-league ball, and he turned it down because he wanted to focus on being a quarterback. He improved every season at Nevada. The 49ers drafted Kaepernick with the 36th pick.

Then, in his first season with the 49ers, Harbaugh went with the veteran Smith, who quickly revitalized his career and nearly took San Francisco to the Super Bowl. The Niners flirted with Peyton Manning in the offseason, but pretty much everybody flirted with Peyton Manning in the offseason. Even Brent Musburger.

When this season opened, Harbaugh went with Smith again. This was an obvious choice. Everybody knew Smith had been very good. Kaepernick was completely untested. Surely, the 49ers could see the same things in practice that we see now -- Kaepernick can beat defenses in more ways than Smith can. But he hadn't shown it in a game, and Smith was playing so well (70.2 completion percentage, 104.1 quarterback rating).

But then Smith suffered his concussion, Kaepernick blew away the Bears, and Harbaugh decided that was enough. You could tell by some of the San Francisco players' public comments that they were amazed by Kaepernick's command of the huddle, and of the game. So Harbaugh went with Kaepernick.

Kaepernick's stats (62.4 completion percentage, 98.3 rating) are pretty close to Smith's. He has shown greater playmaking ability than Smith -- and, as you might expect from an inexperienced player, he has made a few more mistakes.

And this is where we get to that stat I mentioned earlier.

On Nov. 25 against the Saints, Kaepernick threw a second-quarter interception. He didn't get the ball again until the third quarter, but when he did, he led the 49ers on an 80-yard touchdown drive. He finished it with a six-yard touchdown pass to Frank Gore.

On Dec. 16 against the Patriots, Kaepernick threw his second interception of the season. The 49ers got the ball back on the New England three and ran for a touchdown, so that doesn't really factor into this discussion. But Kaepernick's first pass after the interception was a 27-yard touchdown pass to Michael Crabtree.

On Dec. 23 against the Seahawks, Kaepernick threw his third interception of the season. (It was picked off by Seahawks corner Richard Sherman, who presumably did not stop talking for the entire play.) The next time he got the ball, Kaepernick led the 49ers on a 90-yard touchdown drive, capped by his 18-yard touchdown pass.

That's three interceptions followed immediately by three touchdown passes. A small sample size, I know. But there is more:

On Dec. 2, Kaepernick was called for intentional grounding in the end zone, giving the Rams a safety. He responded by leading the 49ers on a 94-yard drive that ended in a field goal.

In that same game, Kaepernick fumbled on a lousy play call -- the 49ers ran a risky option-pitch in their own territory with a 10-2 lead. The Rams scored and tied the game. Kaepernick immediately led the 49ers on a 65-yard drive that ended in a field goal.

This is still not a huge sample size. But those are the five most deflating plays that Kaepernick has made since he became a starter, and he followed them up with five scores: three touchdown drives and two long field goal drives.

That is a player who can handle the pressure of playing quarterback for a championship contender. And again: The 49ers might lose this weekend, and Kaepernick might have a lousy game. Tom Brady, Peyton Manning and John Elway have all had lousy playoff games. Smith could have had one, too.

But if Harbaugh had stuck with Smith, the 49ers would not be as dynamic now, and they still would not know if Kaepernick was the long-term solution. They would have to bring Smith back as the starter for next season, at considerable (but certainly not outrageous) expense. Now they can trade Smith for draft picks, and they can go into next season, and probably the next 10, knowing Kaepernick is capable of leading them.

The best franchises in the NFL make smart decisions before they are obvious decisions. This is why the Patriots have stayed in contention for more than a decade. And this is why Harbaugh was right to choose Colin Kaepernick over Alex Smith.

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