Colin Kaepernick benching is the end of an era for 49ers

Is Kaepernick's time with the 49ers over? (2:09)

Adam Schefter explains what Colin Kaepernick's benching means for his future with the 49ers. (2:09)

SANTA CLARA, Calif. -- Colin Kaepernick had been playing scared, for lack of a better term, since the Week 3 debacle against the Cardinals in Arizona, when he threw four interceptions, including a pair of pick-sixes, and the San Francisco 49ers lost by 40 points.

He was not playing with his usual reckless, somewhat breathtaking abandon; instead, he said he was not going to force passes and put his team into bad situations.

Gone was the bravado that launched his signature Twitter hashtag of #7tormsComing this offseason, when he worked on his skills as a pocket passer with two-time NFL MVP Kurt Warner. Instead, a kinder, gentler, humbler quarterback took his place, at least in the eyes of the media.

And Kaepernick’s play suffered. Mightily. Enough for the Niners to bench him in favor of Blaine Gabbert for this weekend’s game against the Atlanta Falcons.

It was a year ago when then-coach Jim Harbaugh -- the guy who made Kaepernick his hand-picked QB over a very popular-in-the-locker-room Alex Smith -- tried to mold Kaepernick into more of a traditional quarterback. The experiment failed.

And with Harbaugh gone, who would protect Kaepernick in Santa Clara from himself?

Because as the losses piled up and the stats became more unseemly -- the Niners have the worst offense in the NFL, and their 109 points scored is the fewest in the league -- whispers of Kaepernick’s act in the locker room became audible grumbles.

A shy kid to his supporters, an arrogant loner to his detractors, Kaepernick -- with his ever-present headphones -- was reportedly called out in a team meeting by Vernon Davis, who was traded Monday. Which also begs the question: Is this the best way for the Niners to reclaim a thus-far lost season, sitting 2-6 and in last place in the NFC West, four games behind the Cardinals?

It feels more like an admission that this is the end of an era, and really, I’m not so sure they believe Gabbert is the answer going forward, either.

With Davis shipped to the Denver Broncos and Kaepernick benched, the Niners now have only three starters in their same position from Super Bowl XLVII a mere three seasons ago: left tackle Joe Staley, outside linebacker Ahmad Brooks and inside linebacker NaVorro Bowman, while Alex Boone has shifted from right guard to left guard.

It’s a wake-up call for Kaepernick, though with how team-friendly his contract is, parting ways with him, à la Harbaugh’s exit, might be the only logical next step.

After all, the manner and frequency with which coach Jim Tomsula seemingly went out of his way to heap praise on Gabbert in training camp made many observers wonder why the rookie coach was pumping up a backup quarterback so feverishly.

Was the groundwork being laid for this day, a few hours shy of Kaepernick’s 28th birthday?

Not if Kaepernick had won more games, and maybe won over the locker room.