SANTA CLARA -- Colin Kaepernick laughed, he barked orders, he threw missiles, and when he gestured, his teammates moved wherever he told them to go.

Simple summary: The 49ers quarterback was in command out there on Wednesday, in absolute command physically and vocally.

This was just one drill, in a May workout, with no Seattle defensive players anywhere in sight.

But Kaepernick's crisp demeanor and easy confidence was something very different and very revealing.

At one point, he seemed to take over the entire session, including curtly waving off backup Blaine Gabbert's turn so Kaepernick could throw another red zone rocket to Michael Crabtree.

San Francisco 49ers’ starting quarterback Colin Kaepernick (7) looks to shakes hands with other players following their 34-24 win against the Atlanta
San Francisco 49ers' starting quarterback Colin Kaepernick (7) looks to shakes hands with other players following their 34-24 win against the Atlanta Falcons at Candlestick Park in San Francisco, Calif. on Monday, Dec. 23, 2013. (Nhat V. Meyer/Bay Area News Group) ( Nhat V. Meyer )

And I don't think Gabbert, quarterbacks coach Geep Chryst or receivers coach John Morton minded a bit.

Kaepernick is in charge, and he doesn't mind everybody else noticing this.

"I really expect a real breakout year for Colin," coach Jim Harbaugh said.

"Athletically, he looks bionic. And if you all remember 'The Six Million Dollar Man,' that's what it looks like to me.

"He's very gifted, he always has been; he has the look and feel of a guy who's really going to break out, even more so than he already has."

Kaepernick, of course, has been through some things in the last few months, starting with his interception to climax the 49ers' NFC Championship game loss in Seattle and continuing to the odd incident and police investigation in Miami.


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The Miami situation seems to be close to resolution without any charges filed, and Kaepernick said he just wants the matter closed.

"I did nothing wrong in that incident," he said Wednesday.

It's tricky to extrapolate anything from such a hazy description of events; but if anything, getting past the Miami situation and onto the field seems to have pushed Kaepernick to a more sturdy place.

He has two new veteran receivers -- Brandon Lloyd and Stevie Johnson (who had a minor injury and missed Wednesday's session) -- to add to Anquan Boldin and Crabtree.

He's in his second full offseason as the 49ers' starting QB; he's in line for a huge new contract extension at some point this summer, if the negotiations go well.

And Kaepernick has never looked or sounded more comfortable in the role of Franchise QB.

"I think this is the time of year where you can be vocal and you can work on things a lot more because you don't have to play Sunday," Kaepernick said in a breezy, loose 10-minute session with reporters.

"So if you want to experiment with things, if you want to try things out, now is the time that we want to do that and see if we can get something new that's going to work for our offense."

Is he finding that his teammates want to hear him speak loudly?

"It's not necessarily always me trying to give advice or necessarily command things," Kaepernick said.

"It's a lot of times just a conversation as far as, 'What are you seeing? How would you run this route?' Especially with someone like Brandon and Stevie."

To that point, Kaepernick said there was a specific reason he was talking so much with Lloyd during the red zone drills.

Lloyd has scored a lot of touchdowns in his career, so why not tap his expertise?

"I think that's something that we know we've struggled with here -- the red zone," Kaepernick said. "And that's something we're constantly trying to improve.

"And he's had success down there. So if there's something we can pick up from him, how he runs routes, how he sets things up, that's something we want to take and try to make it ours."

You can't put it any more clearly than that; the truth is, Kaepernick has often avoided saying anything as clearly as that during his first few seasons as the 49ers QB.

But, as Harbaugh suggested, when a top QB comes into his own, the world opens up.

It also helps that the 49ers have provided Kaepernick with a stronger set of receivers just in time for the personal blooming.

"Kap said it the other day, he feels that he has a stable of receivers now," Harbaugh said. "Maybe that's the first time that we've said that since we've all been here together. And I concur. It feels that way."

Back in March, 49ers CEO Jed York and general manager Trent Baalke both said they understood that Kaepernick's market value was extremely high, and they hoped to sign him to a long-term extension before the start of training camp.

Colin, any thoughts on where things stand now?

"I'm just letting my agents handle that," Kaepernick said. "I'm playing football regardless."

He said this with a big smile, which added all the emphasis necessary. Kaepernick knows that if he takes command of the 49ers offense, everything will take care of itself.

Which all seems to be happening now.

Read Tim Kawakami's Talking Points blog at blogs.mercurynews.com/kawakami. Contact him at tkawakami@ mercurynews.com.