
Sixteen months ago, the 49ers had every reason to believe Colin Kaepernick was their franchise quarterback.
He had all the obvious physical tools as part of the first wave of dual-threat quarterbacks. And he experienced successes in the postseason, engineering a franchise-record three road playoff victories -- more than Joe Montana and Steve Young, combined.
Yet, the 49ers did not go all-in on the investment with a $115 million contract extension through the 2020 season that was agreed upon in June 2014.
Stay in the game with the latest updates on your beloved Bay Area and California sports teams! Sign up here for our All Access Daily newsletter.
With a relatively low signing bonus of $12.3 million and no other fully guaranteed money, the 49ers left themselves the flexibility to cut ties with Kaepernick at virtually any point.
After two alarming performances the past two Sundays while the 49ers scored a combined 10 points in losses to Arizona and Green Bay, Kaepernick’s future with the organization beyond the current season is in serious doubt.
[MAIOCCO: Warner: 49ers' Kaepernick 'learning under the gun']
Kaepernick is scheduled to earn $14.3 million in salary and bonuses next season. Is he playing like a quarterback worth that hefty price tag? If the 49ers decide to move on from Kaepernick after 12 more regular-season games, it would actually save the 49ers more than $9 million in cap room.
San Francisco 49ers
Find the latest San Francisco 49ers news, highlights, analysis and more with NBC Sports Bay Area and California.
Coach Jim Tomsula said Monday the 49ers staff constantly evaluates all players. When asked if the team is evaluating whether Kaepernick should remain as the starter, he answered, “I don’t want to say it then that starts a whole. . . that’s not where I’m at. I don’t want to say that, no.”
The 2015 San Francisco 49ers are not being labeled as a rebuilding project for one simple reason: Their quarterback is no longer a youngster.
Kaepernick turns 28 in a month. He has 49 career NFL starts, including six in the postseason. The 49ers already know a lot about Kaepernick, but they need to make sure the decision at the end of the season is clear-cut.
The 49ers promised to run the ball more this season, and that’s exactly what Kaepernick is doing. With 195 yards rushing on 33 attempts through four games, Kaepernick is on pace to rush for a career-high 780 yards.
However, he is also on pace for his worst passing season since entering the starting lineup in place of Alex Smith in the middle of the 2012 season.
The 49ers signed speedy wide receiver Torrey Smith to a five-year, $40 million contract this offseason but have been unable to get him involved when games are still in reach. Smith and Anquan Boldin, who were teammates of quarterback Joe Flacco with the Baltimore Ravens, were visibly angry the way the past two games have unfolded.
On Monday, Smith claimed he and Boldin are on the same page with Kaepernick. But, he said, they have been unable prove it in the games.
“That has to change or we’re not going anywhere,” Smith said. “We have to get that right between the quarterbacks and the passing game, in general. If you can’t pass the ball in 2015, you’re in trouble.”
And regardless of everything else that might be happening with the team, that falls on the quarterback.
The offensive line has not played at a consistent level – an epidemic around the NFL that is not unique to the 49ers. Kaepernick generally holds the ball too long whether there is pressure or a clean pocket from which to throw.
“Certain routes, you don’t have to have all the time in the world,” Smith said. “There are things we can do to make it happen, but we just have to be confident at it and get some rhythm going.”
Confidence and trust in one another is lacking throughout the offense. Players wonder if offensive coordinator Geep Chryst is putting them in the best positions to succeed. Kaepernick is frustrated because of what's going on around him. His teammates are clearly frustrated in him, too. It becomes a vicious cycle.
Kaepernick was intercepted four times against the Cardinals. His first two passes were late coming out of his hand and were returned for touchdowns. The scars from those plays were still noticeable a week later with his cautious decision-making against the Green Bay, which played a large portion of the game with no safety in the middle of the field.
[MAIOCCO: Frustrated Niners: Kaepernick overcorrects, takes no chances]
“Some of them were protecting throws,” Kaeperick said afterward of his 12 incomplete passes, some of which were not even close to his nearest receiver. “I’m not just going to throw a ball into coverage.”
Four of Kaepernick’s passes intended for Smith and Boldin against single coverage sailed out of bounds. Three of his attempts were thrown into the ground. Two of his passes were behind his intended target. His one interception was an under-thrown deep ball to Boldin. And two passes were dropped, including a well-thrown fade to a leaping Smith in the end zone.
The 49ers need to find out if Kaepernick has what it takes to pull himself out of this mess. That’s why the 49ers should not – and, apparently, will not – bench Kaepernick in favor of backup Blaine Gabbert heading into their game Sunday at the New York Giants.
At the quarterback position, it becomes an organizational decision that must include coach Jim Tomsula but, more important, CEO Jed York and general manager Trent Baalke.
In six drafts, the only quarterbacks Baalke has selected were Kaepernick and B.J. Daniels, a seventh-rounder in 2013. Gabbert, the 10th pick in the 2011 draft, came to the 49ers in a 2014 trade. Gabbert is likely more of a stop-gap, rather than a long-term answer if the 49ers move on from Kaepernick.
The 49ers have to know one way or the other with Kaepernick before arriving at a difficult offseason decision. After his performances of the past two weeks, the outcomes appears heading in one obvious direction. But the organization must continue to ride it out -- for at least another week.
It’s a difficult balancing act. The 49ers have to stick with Kaepernick for a while to see if he can pull himself together and be the quarterback who looked like the future of the organization before last season.
But they also have to gauge the temperature in the locker room and not let things go too far before it completely rips the team apart.
After all, once Kaepernick is demoted to the sideline in favor of Gabbert, it’s a foreshadowing that the organization’s offseason decision has already been made.