Colin Kaepernick over Alex Smith? This is unconventional, daring, potentially brilliant, potentially devastating, and so predictably Jim Harbaugh.

The 49ers coach is like the Claire Danes character in the Showtime hit series "Homeland." She's smarter and shrewder and more instinctive than many of her CIA peers, and as it turns out, her suspicions about a certain domestic terrorist were right all along. So, OK, she's also a little crazy.

We're not suggesting Harbaugh is crazy, only that he operates in a more unusual and dramatic realm than most NFL coaches. He can be tightlipped and parse words like a seasoned politician (see Bill Clinton) in the same sentence. Rex Ryan is another example of an outsized NFL weekly drama, but the difference is that Harbaugh took over as a rookie a season ago and immediately transformed an organization.

Harbaugh hasn't hit a slump yet, either; he led the 49ers a year ago to a 13-3 record, restored the luster to a slumping franchise and revived Smith's career, all while not-so-secretly plotting for a future with Kaepernick as his quarterback.

Again, none of this is a surprise. New bosses often hire their own people.

Harbaugh – a rookie the same year as Kaepernick, the 49ers' second-round draft choice out of Nevada – has long been tantalized by the new-age dimensions the 6-foot-4, 230-pounder offers. Mobility. Escapability. Big-play capability. The ability and willingness to throw deep, to make the offense more vertical than at any time since the Steve Young era – long before the franchise went sideways.

Harbaugh's assessment of his quarterbacks was evident almost from the moment he stepped onto the team's practice facility in Santa Clara. Clues, hints, tips. They were all there, beginning with how long it took to name Smith his starter, the flirtation with future Hall of Famer Peyton Manning, Kaepernick's sudden appearances earlier this season on crucial possessions, regardless of whether or not the shuttle system was disruptive to Smith.

Before suffering a concussion, Smith was leading the NFL in completion percentage and had guided the 49ers to a 6-2 record. Smith, an efficient, mistake-averse performer – characteristics often associated with teams dominated by their defense – has taken more hits than a crash dummy, yet he kept coming back for more.

Forget loyalty or appreciation or any of that touchy-feely stuff. The NFL is an emotionally and physically crippling league, and the super-intense Harbaugh understands that better than most. During his 15-year NFL career, he was a starting quarterback and a bench warmer. He was traded and injured, was named the winner of a controversial quarterback duel in Chicago and, since taking over the 49ers, has been more hands-on than most head coaches.

At practices and before games, he routinely demonstrates what he wants by taking the snaps and making the throws.

And when you win, you can do and say almost anything. Or say very little.

"It'll be our plan to start Colin and prepare him to make that start this week against the Rams," Harbaugh said during Wednesday's news conference. "The rationale is you've got two quarterbacks that we feel great about as the starting quarterback. Both have earned it. Both deserve it. Alex over a long period of time; Colin by virtue of the last three games. What tips the scale is Colin, we believe, has the hot hand and we'll go with Colin. … And we'll go with Alex. They're both our guys."

Come again? Confused? Harbaugh loves to mess with people, to keep everyone, including the opposition, guessing. Game planning for Smith is significantly different than preparing for Kaepernick.

While an injury or a flop by Kaepernick could give Smith yet another chance to convince his coach that he gives the 49ers the best chance to get to the Super Bowl, Harbaugh will give Kaepernick every opportunity to establish himself as the starter and prove he made the right call.

Smith's career arc just took another downward spiral, perhaps for a final time in the Bay Area.

Right or wrong, brilliant or imprudent, Harbaugh feels Kaepernick is the future, and he says the future is now.

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