San Francisco 49ers starting quarterback Colin Kaepernick has had an unusual career to this point.

After not starting a single game during his rookie season, the 2011 second-round pick failed to oust Alex Smith ahead of his second season. Kaepernick may never have seen the field for the 49ers in a starting role if Smith hadn’t suffered a concussion halfway through the 2012 regular season.

That injury set in motion a chain of events that ultimately stopped five yards short of being a fairy-tale beginning to Kaepernick’s career.

He immediately showed a comfort and fit in the 49ers offense that allowed him to make the unit more dangerous than it had ever been with Smith at the helm. In what essentially equaled eight full games, Kaepernick threw for 1,814 yards while completing 62.4 percent of his passes. He had 15 total touchdowns, with just three interceptions and two lost fumbles (nine total).

In the playoffs, that effectiveness continued despite his lack of experience. It continued to the point that he would start in the Super Bowl.

Fittingly, the Super Bowl came down to the final two minutes, and Kaepernick would be tasked with winning the game for his side. On 4th-and-5, down by five with one minute, 50 seconds left in the game, then-head coach Jim Harbaugh put Kaepernick in the pistol formation and called a passing play.

That passing play tasked Kaepernick with throwing a fade route to his best wide receiver, Michael Crabtree. Crabtree would never get a chance to catch the football, though.

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With a play that went completely against the theme of his career, running back Frank Gore appeared to be the unreliable one at the most important moment of the game for the 49ers. Gore seemingly blew his blitz pickup by shifting to the wrong side of the offensive line, leaving Kaepernick immediately under pressure from a free rusher.

As a result, he rushed his throw and pushed the ball too far for Crabtree to win it over the defensive back covering him. It was a divergence in the path of Kaepernick that likely altered a lot over the coming years for the 49ers.

Making that play may not have prevented Harbaugh from leaving this past offseason, but it likely would have smoothed out some of the issues between he and general manager Trent Baalke. More significantly for Kaepernick, he had less leverage in contract negotiations without the Lombardi Trophy sitting beside him.

He still signed a huge contract extension around 12 months after losing in the Super Bowl, but it was a team-friendly deal that gave him limited long-term security.

The initial reports suggested that Kaepernick agreed to a six-year deal worth an incredible $126 million. However, once the actual details of the deal emerged, it became clear that the contract was bloated with conditions that actually made much of the guaranteed money a fallacy.

As such, Kaepernick’s security only extended for two years. 

He signed that deal in June 2014, after a relatively impressive first full season as a starter. Kaepernick didn’t reach the spectacular heights that he had in 2013, but he had shown enough within the construct of the 49ers offense to be a worthy starter.

In 2014, he undid that work by failing to adjust to a new role in a different type of offense.

Many different narratives can be constructed to explain why the 49ers changed their offense—the friction between the coaching staff and front office, the absence of key offensive linemen, the need to figure out how much Kaepernick could handle—but regardless, the change was made.

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Jim Harbaugh and Greg Roman tweaked their offensive system last year, which led to some of Kaepernick’s struggles.

Before 2014, Harbaugh and then-offensive coordinator Greg Roman had constructed the perfect offensive strategy for Kaepernick. It maximized his arm talent and athleticism, while avoiding situations where he had to drop back in the pocket, mitigate pressure and read through progressions.

This offensive design relied on a highly efficient and diverse running game that took the primary focus of the opposition’s setup.

The strength of the running game and design of the offense allowed Kaepernick to excel by throwing to his first receiver regularly, taking open throws in the flat and using diverse, aggressive play action to distort the coverage on the back end of the defense.

In 2014, the 49ers stopped relying on their running game to establish their offense. Gore and rookie Carlos Hyde became complementary pieces who weren’t used enough early in games. According to Football Outsiders, the 49ers ran on first down over four percentage points less often in 2014 than they did in 2013.

Without relying on the running game on early downs, Kaepernick was put in situations where it was easier for the defense to be more aggressive with their pass rush and their coverages. He also had to hold the ball for longer between the tackles and couldn’t rely on designed rollouts.

This shifted the focus onto Kaepernick’s footwork, eye level and ability to read coverages.

Footwork and Eye Level

Eye level and footwork are tied together because that is often how they work on the field.

A quarterback with poor feet in the pocket is more likely to look to run and drop his eyes from his receivers downfield with greater regularity. While Kaepernick has great straight-line athleticism, he doesn’t have a fluid body or subtle feet. This means managing the confines of the pocket becomes an adventure.

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Until the NFL implements live, widespread All-22 angles to watch games, the impact of poor footwork and eye level will likely be lost on most onlookers. That is because you can’t see what is happening downfield against the defense’s coverage with the angle that is used on broadcasts.

That is fortunate for Kaepernick because he left a large number of yards on the field in 2014 by missing open receivers downfield.

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On this play, Kaepernick actually makes a smart initial move by stepping up to better position himself against the edge pressure coming from his right. He can step up in the pocket because the Kansas City Chiefs have only sent four rushers after him.

He appears set to deliver the football from the perfect spot within the pocket, but this is where his flaws come into focus.

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Kaepernick stopped his throwing motion before releasing the ball and hesitated. He wasn’t comfortable making an anticipatory throw, so he dropped his eyes away from the two receivers downfield who were running into clear space.

He wasn’t under pressure in the pocket; he just needed to reset his feet and establish his base to survey the coverage once again.

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Instead, Kaepernick immediately looked to scramble into the running lane that presented itself in front of him. His movements are too elaborate and aggressive in the pocket. It means that while he can sometimes step up to avoid edge pressure, that initial movement is the end of his adjustments.

On this play specifically, Kaepernick ran for a two-yard gain, while his receivers ran into space 30 yards downfield.

Receivers in San Francisco looked much worse than they were because of plays like these. The 49ers added Brandon Lloyd and Steve Johnson in the offseason to help Kaepernick, but both players required their quarterback to work to the design of the offense to be productive.

Passing plays are designed to work to a specific timing with the ball coming from the middle of the field. If your quarterback is panicking in the pocket and taking his eyes away from the coverage, he can’t run the offense as it’s supposed to be run.

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Taking long strides, dipping your hips, turning your shoulders and dropping your eyes are chronic issues for quarterbacks who struggle in the pocket. Kaepernick showed all of them off on a regular basis last season. He not only couldn’t mitigate pressure, but he also regularly ran himself out of clean pockets and into pressure.

Running out of clean pockets can be negated if the quarterback is athletic enough to scramble for first downs or make throws outside of the pocket. That is significantly easier to do on 3rd-and-2 or 2nd-and-5 instead of 1st-and-10, 2nd-and-10 or 3rd-and-7.

It’s easy to blame the system change and the coaching staff for putting too much pressure on Kaepernick, but they didn’t ask him to do anything outlandish.

He wasn’t put in a position where he needed to orchestrate the offense like Drew Brees or Peyton Manning in his prime. He was expected to execute to a degree no different than every other quarterback in the NFL, yet he couldn’t do it.

The limitations Kaepernick showed should actually create more appreciation for what the 49ers managed to get out of him in previous seasons.

Reading Coverages

As Robert Griffin III found out this past season, an altered scheme with new assignments can completely alter how a quarterback must play the game. Griffin III received a huge amount of criticism for his inability to adjust to a more traditional passing attack, but Kaepernick arguably struggled more.

The 49ers starter doesn’t anticipate receivers coming open against any kinds of coverages ,and he doesn’t diagnose blitzes quickly at the snap. Those are major issues, but arguably the most concerning aspect of his play is his tendency to predetermine passes so often.

Despite throwing just 10 picks last year, Kaepernick fired out 22 interceptable passes. Fifteen of those were considered bad decisions, while at least four appeared to be a result of predetermined throws.

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On this play against the Philadelphia Eagles, it’s 3rd-and-3 with Kaepernick in the shotgun and receivers spread across the formation. Before the beginning of the play, the offense motions tight end Vernon Davis across the formation.

Safety Nate Allen follows Davis, so Kaepernick is immediately reading man coverage.

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Both receivers to the right of the screen are running slants against press-man coverage. Kaepernick understands that he should have a receiver open against man coverage to this side of the field. Anquan Boldin gives him that open receiver working against Malcolm Jenkins in the slot.

However, Kaepernick looks directly through Boldin when he wins at the line of scrimmage and instead holds the ball waiting for Brandon Lloyd outside.

Lloyd also wins in his route, but Kaepernick throws the ball straight to Jenkins. Jenkins was able to pass Boldin on inside and read Kaepernick’s eyes to stand directly in his passing lane. Kaepernick didn’t read his receivers as they released into their routes; he decided before the snap that the ball was going outside.

Ultimately, his predetermined throw is what allowed Jenkins to create the turnover and run it back for a touchdown.

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On this play, the Chiefs are threatening to blitz but have kept both safeties in relatively deep positions. As Kaepernick catches the ball from his center, he initially appears to direct his eyes toward the safety to the right side of the offense.

Kaepernick’s receiver to that side of the field is running a slant against press coverage.

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Whether Kaepernick looked directly at the safety is unclear, but he did move his eyes toward his intended target gradually. This allowed the safety to read his eyes and close on the receiver aggressively. He was in position to break on the ball before it arrived to the receiver.

If the safety, Ron Parker, had shown off better hands, he would have had an interception.

When the 49ers were at their peak with Kaepernick, slants were an important part of the offense because opponents would often be reluctant to play press coverage or fully focus on trying to read the quarterback. They were too afraid of the 49ers’ commitment to the running game and their prowess doing it.

Each of Kaepernick’s four obviously predetermined plays appeared similar, with the final two coming in separate games against the St. Louis Rams.

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No matter the scheme the 49ers run moving forward with Kaepernick, he can’t afford to make decisions such as these. It’s too simple for defensive backs to read what he is doing and break on the ball if he is repeatedly predetermining his throws.

Even with these established flaws, Kaepernick should still be able to hold onto his starting role with the team if he can show off better accuracy than he did in 2014.

The quarterback still made a number of exceptionally difficult passes last year, but his consistency from snap to snap left a lot to be desired in comparison to 2012 and 2013. Much of that inconsistency can be traced back to his woefully bad mechanics.

Kaepernick has apparently worked to correct his mechanical issues during the offseason:

#49ers Colin Kaepernick new throwing motion, to my untrained eye, looks tighter & faster with better grip pic.twitter.com/9vJAXiYCWw

— Cam Inman (@CamInman) April 29, 2015

While that throwing motion is ideal and dramatically improved over what was typical through last season, it’s not a sure sign that his problems are corrected. Plenty of quarterbacks with bad mechanics make huge efforts in the offseason to correct the issue but then revert back to what is natural when pressured in games.

If Kaepernick can’t carry over his new throwing motion into the regular season, it’s likely that his accuracy will once again be a major issue. That’s not something he can afford to endure as he enters what is most definitely a make-or-break season.