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Colin Kaepernick is the 49ers starting QB again. Now what?

There are so many questions to answer as the 49ers make a change at the most important position on the field.

NFL: Dallas Cowboys at San Francisco 49ers Kelvin Kuo-USA TODAY Sports

When we last talked about Colin Kaepernick’s on-field performance, he was somehow simultaneously getting benched for one of the worst starting quarterbacks in NFL history while also receiving favorable comparisons to eventual NFL MVP Cam Newton, which is all just very bizarre to think about.

Multiple offseason surgeries, a new coaching regime, and 13 miserable Blaine Gabbert starts later, Kaepernick has been inserted back into the lineup as San Francisco’s starting quarterback, as head coach Chip Kelly announced earlier this week.

Any time you have change at the game’s most important position, there are a number of factors worth considering. Let’s run through some of the more pertinent questions surrounding the 49ers’ quarterback change and see if we can get an idea of what to expect over the final 11 games of the season.

Why make the change now?

It’s been an ugly five-game start to 2016 for Gabbert and the 49ers offense. San Francisco is averaging a league-worst 23.5 yards per drive; no other team is averaging fewer than 25.0 yards per possession. While certainly not the only problem, Gabbert and San Francisco’s 30th-ranked pass offense DVOA—which surpasses only the Dolphins and Texans so far—have been at the nucleus of their issues offensively.

Gabbert’s deficiencies are numerous, but his inaccuracy has been the most glaring. Open receivers are routinely left watching passes sail far outside their reach (if the ball even travels their direction to begin with), not only leaving big plays on the field, but often putting the ball back into the opponent’s hands in crucial situations.

After a turnover-free season opener, Gabbert has thrown six interceptions over the past four games, and his 4.0 percent interception rate tops only Ryan Tannehill and human-turnover-factory Ryan Fitzpatrick after five games. That number make sense for a bad quarterback with a gunslinger mentality like Fitzpatrick, who often appears to be actively trying to put the ball in harm’s way. But for a hyper-conservative quarterback like Gabbert, who rarely seems willing to take risks and push the ball downfield, that number looks even worse.

Interceptions against the Panthers and Seahawks were largely inconsequential, as they came late in games that were long decided. Over the last couple weeks, however, Gabbert’s errors have secured defeat in otherwise winnable contests. An interception early in the fourth quarter against Dallas gave the Cowboys the ball on what should have been a go-ahead touchdown pass to Torrey Smith. Last week, a pair of Gabbert interceptions gave the Cardinals short fields, which they converted into 10 points in a game where Drew Stanton & Co. failed to move the ball consistently when they weren’t effectively starting drives in the red zone.

None of these issues are new for Gabbert. His career 3.0 percent interception rate is considerably higher than league average—which has fallen between 2.3 and 2.5 percent over the past three seasons—and his career 56.1 completion percentage also falls well short of anything resembling league average performance. Over the course of six NFL seasons and 1,216 passing attempts, Gabbert has consistently shown us he’s simply not an accurate passer. At some point, it becomes unreasonable to expect that player to suddenly become something different. In Gabbert’s case, he’s proven to be no more than a backup quarterback who might be capable of holding things together for a spot start or two on the right team.

Kaepernick’s track record at this stage paints a picture that is far more muddy. As recently as 2013 he appeared to be one of the league’s next great quarterbacks, but has since seen his performance fall sharply. Chip Kelly and his staff know what they have in Gabbert; they need to find out if there’s any hope of revitalizing Kaepernick.

Where can Kaepernick be an improvement over Gabbert?

The simple answer is not all that different from the appeal of Kaepernick when he retained the starting job over Alex Smith back in 2012 even after the latter had returned to health: The ability to generate more big plays.

Gabbert’s only real saving grace this season has been the value he’s added in the run game. According to ESPN’s expected points added numbers, Gabbert has added the third-most rushing value of any quarterback this season, trailing only Tyrod Taylor and Aaron Rodgers.

It’s difficult to imagine there being a large drop-off with Kaepernick in the lineup, however. Most of Gabbert’s value on the ground has come from scrambles rather than on zone-read keeps, where he seems to often find himself sliding to the turf two or three yards beyond the line of scrimmage. It seems reasonable to think even a diminished Kaepernick can maintain that sort of performance in this offense, while also offering greater potential for big plays should the opportunity present itself.

More importantly, Kaepernick offers the potential to connect on more downfield throws in the passing game. Kaepernick’s clear strength as a passer early on was his downfield accuracy. As I wrote about back near the end of the 2014 season, Kaepernick’s completion percentage on passes traveling 15 or more yards in the air over the 2012-13 seasons (47.4 percent) was the fourth-best mark among the 32 quarterbacks who had thrown at least 75 such passes. It’s easy to forget now, but Kaepernick was once a player dropping dimes like this in playoff games:

It’s been a while since we’ve seen that player; the crux of that article from 2014 was about how the 49ers’ deep passing game had fallen off a cliff that season. While Kaepernick’s deep completion percentage bounced back somewhat in 2015, other issues (some of which we’ll get to) prevented it from mattering all that much. There’s certainly no guarantee we’ll consistently see throws like that from Kaepernick over the rest of the season, but we’ve at least seen Kaepernick do it for an extended stretch, which unfortunately is more than we can say for Gabbert at this point.

Where is Kaepernick potentially worse than Gabbert?

It’s a scary thought, I know. But while it might be a low bar for Kaepernick to hurdle to wind up being an improvement over Gabbert’s performance through five games, that certainly doesn’t mean he’s a lock to be an improvement across the board.

Perhaps Kaepernick’s biggest struggle, really throughout his career, has been his inability to effectively move within the pocket to deal with pressure. When re-watching some of his throws from those 2012 and 2013 seasons, the thing that stuck out most after his accuracy was just how much time he had in the pocket to deliver some of those throws. But as the 49ers’ offensive line declined over subsequent seasons, so did Kaepernick’s play.

Pass protection is often as much on the quarterback as it is on the offensive line. Though at times it led to missing open players downfield, Gabbert typically got the ball out of his hand quickly, which can significantly help the offensive line. Kaepernick hasn’t always provided the big guys up front with much help. According to Pro Football Focus’s data, Kaepernick posted one of the league’s highest average time to throw marks during each of his seasons as a starter. Part of that is due to his mobility and ability to scramble and extend plays, but it was also a result of simply hanging on to the ball too long on many plays.

During his final season-plus as a starter, plays like this popped up far too frequently:

Rather than stepping up in the pocket—allowing Joe Staley to run his man out of the play—and making a quick throw to one of two open options in the middle of the field, Kaepernick hangs on to the ball and just sort of drifts backward right into a sack.

Other times, Kaepernick just has trouble knowing when to give up on a play and get the ball out to his checkdown. One might say Gabbert was a little too good at this particular trait, but it’s never something Kaepernick has excelled at even when playing his best.

While the offensive line has looked better in pass protection this season than it did at just about any point over the 2014-15 seasons, Kaepernick will need to avoid plays like these if that has any chance of continuing.

What should we expect from Kaepernick in 2016, in this offense?

To me, this is really the most intriguing question: How does the marriage of Kaepernick and Chip Kelly actually play out on the field? I’ve never been completely sold on the idea that this is the match-made-in-football-heaven some have made it out to be, but there’s no question it will interesting to see play out. The ceiling for the best-case scenario is incredibly high, even if it’s not especially likely.

Aesthetically, Kelly’s offense looks nothing like the one Kaepernick excelled in under Jim Harbaugh. Despite that, there are a number of broader similarities that could potentially help the quarterback in the same way.

Both offenses are run-first by design—despite spending a large portion of their games trailing this season, the 49ers have the most run-heavy offense in football so far. Both offenses feature a high percentage of play action, which helps to pull up the linebackers and open up space for those intermediate to deep throws Kaepernick has had success with when playing his best. And like Harbaugh, Kelly has a track record of elevating the play of middling quarterbacks.

It’s easy to talk yourself into all of this working out and Kaepernick revitalizing his career under his new coach. But even if Kaepernick bounces back and begins to approximate his level of play from early in his career—which is a lot to ask—a dearth of offensive talent makes it difficult to envision this offense being anything more than mediocre. That’s a solid step forward for an offense that currently ranks 22nd in DVOA, but it’s not as if San Francisco is about to start ripping through the league on their way to the playoffs, even if things go as well as could reasonably be expected.

The reality is no one has any idea how this is going to play out. Kaepernick has effectively been two completely different players over the course of his career, and his career trajectory is near unprecedented. There’s not a blueprint out there for a quarterback who produced like one of the league’s best to start his career before falling off a cliff for what should have been his peak seasons.

The most likely outcome probably involves both Kaepernick and the 2016 49ers continuing to be not very good at football. But considering how bad Gabbert has looked to this point, it’s clearly a move that needed to happen. And for at least a couple more days, it will remain fascinating to think about what Kaepernick and Kelly could be.