Pete Carroll’s defense doesn’t often stray too far from their core stuff, believing that their personnel is going to beat you more often than not. And in last week’s 19–3 defeat of the 49ers, Seattle did exactly what you would’ve expected.

The Seahawks played almost exclusively with a single safety in the deep middle of the field (usually Earl Thomas), primarily running their press Cover 3 zone while also mixing in some man coverage here and there. The Seahawks rushed four on most snaps, blitzing on just seven of Kaepernick’s 36 drop-backs according to Pro Football Focus.

There was nothing that Seattle showed schematically that Colin Kaepernick & Co. shouldn’t have been prepared for. Yet, Kaepernick was seemingly unsure of where to go with the football on most plays and misfired on throws when he did eventually pull the trigger, leaving numerous plays on the field in the process.

On the first play of San Francisco’s second possession, Greg Roman dials up a four verticals play from a balanced, two tight end set. Against Seattle’s Cover 3, the area to attack is the two-on-one advantage the 49ers have in the middle of the field against Earl Thomas.

As Kaepernick hits the back of his drop, both Vernon Davis and Garrett Celek are clearing the second level and coming open down the seams. Earl Thomas is capable of covering more ground than any other safety in football, and it’s understandable to be weary of throwing his direction. But with Kaepernick’s arm strength and Thomas square in the middle of the field, these are throws he should be able to make with relative ease. Ideally, Kaepernick moves Thomas to one side of the field with his eyes before resetting and throwing down the opposite seam — something he’s done on several instances in the past.

Instead, Kaepernick opts to target Brandon Lloyd down the left sideline. Lloyd is unable to adjust to the underthrown pass and the ball falls incomplete. San Francisco would go three-and-out on the drive.

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After two short Carlos Hyde runs to begin the following possession, Kaepernick was faced with a third-and–8 to keep the drive alive. San Francisco has comeback routes on each sideline with Boldin working the middle on a dig route from the slot. Seattle is in their typical three-deep coverage.

Kaepernick begins his drop by looking down the middle of the field, seemingly indicating his first look is to Boldin on the dig route. As Kaepernick hits the back of that drop, Boldin is about to break into a sizable window between the hashmarks.

This would typically be a situation when Kaepernick is at his best — with his first option about to come open into a clear throwing lane for an easy first down throw. Right as you think he’s about to pull the trigger, Kaepernick abruptly snaps towards Lloyd on the right sideline and fires a horribly inaccurate pass that misses to the inside by about five yards, giving Richard Sherman an easy interception.

I’m not entirely sure what Kaepernick is doing here. While he starts the play by looking down the center of the field, the quick snap and throw to Lloyd indicates to me that’s where he wanted to go with the ball all along. However, there’s no reason to hold the safety in the middle of the field — he’s irrelevant on a route to the sideline. Seattle only rushes three on the play, so there’s no need for Kaepernick to hurry the throw.

If you want to stay away from Thomas and throw the comeback, fine. It’s a good route against Cover 3 and Lloyd gets enough separation to make the catch if the ball is delivered accurately and on time. But why not look that direction earlier, check the coverage, and allow yourself to more easily make an accurate throw to the sideline? The thought process here just doesn't make a lot of sense. The mistake would set Seattle up with great field position, leading to their only touchdown of the day.

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Fast forward a couple of possessions. Kaepernick starts off the drive with one of his few good plays of the day. With nothing open downfield, he avoids pressure and checks down to a wide open Hyde in the flat for a play that nets 16 yards. It would be San Francisco’s biggest gain all day. After a Gore run was stopped behind the line of scrimmage and another incomplete pass to Lloyd, the 49ers were again facing third-and-long.

Boldin’s motion inside to the trips side gives the 49ers the look they want. Stevie Johnson, aligning with a reduced split, gets plenty of cushion from cornerback Tharold Simon on his out route to the first down marker.

Again, this is the type of throw that Kaepernick has excelled at in the past. It’s an easy (for Kaepernick) throw outside the numbers to an open receiver from a clean pocket. But Kaepernick never really sets his feet and throws early, well before Johnson has made his break. Stevie isn’t able to get there and the ball falls incomplete.

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Perrish Cox fumbled away the 49ers’ best opportunity to get points before the end of the first half when he coughed up the ball on a punt return near midfield with 2:36 to go in the second quarter. A three-and-out forced by the 49ers’ defense and a Jon Ryan punt into the end zone gave Kaepernick one more chance to get into field goal range.

The entire possession was mostly a disaster, but a poor decision from Kaepernick ensured the 49ers would head into the locker room empty-handed.

San Francisco comes out in a three-by-one formation, a look they frequently go to in long yardage and two-minute situations. Seattle does a good job of taking away the primary option on the play — Boldin’s corner route from the three-receiver side. Once Kaepernick recognizes this, he moves up in the pocket to avoid the rush and in doing so, gives himself two logical options.

Option A: Throw to Johnson coming open over the middle from the single-receiver side. Stevie likely gets tackled just beyond midfield. The 49ers can then use their final timeout and would still have enough time to try a quick throw to the sideline to give themselves a chance at a long Phil Dawson field goal.

Option B: Kaepernick could also just throw the ball away and try all of this again on the next down. Not ideal, but still probably the second-best potential outcome at this point.

So what does Kaepernick do? He runs, giving himself up with a slide after a measly five yards. The 49ers are forced to use their final timeout and with just six seconds left, any hope of getting a shot at a long field goal is gone.

The chances of San Francisco getting points out of this drive when it began weren’t very good. An inability to move with any sense of urgency made those odds even worse. But a completion to Johnson on that play gives them a chance. Running for five yards was probably the worst possible outcome that didn’t involve a turnover.

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Kaepernick’s poor run-pass decision making was on display again on San Francisco’s opening possession of the second half.

Brandon Lloyd and Vernon Davis are split out to the left of the formation. With Bruce Miller leaking into the flat, the 49ers are looking to work a three-man route combination (curl-wheel-flat) to the wide side of the field.

Kaepernick’s play action fake mostly produces the desired effects. Linebackers Bobby Wagner and K.J. Wright are both pulled up towards the line of scrimmage, creating additional space at the second level of the defense. Kaepernick also gets ample time in the pocket to deliver the ball.

Byron Maxwell stays well over the top in his deep-third zone coverage, which combined with the linebackers getting sucked up by the play fake leaves Lloyd wide open on the deep curl route. Kaepernick has a clear throwing lane; this should be an easy 20-yard gain.

As you can probably guess at this point, there was no 20-yard gain. Kaepernick runs around, briefly considers a throw to a now-covered Lloyd, and eventually decides to take off. He slides near the sideline for a whopping three-yard pickup.

Later in the same drive, with the 49ers in Seahawks’ territory for the first time, Kaepernick makes yet another bizarre decision that might have cost San Francisco a touchdown.

San Francisco calls a nearly identical play to the previous one we looked at with the one difference coming on the route of the receiver to the wide left of the formation. Rather than settling down on a curl route as Lloyd did, Crabtree continues up the seam, pulling Maxwell and Thomas with him.

With Kam Chancellor following Bruce Miller up the field on his wheel route, it should be an easy decision here for Kaepernick. Hyde is wide open in the flat and with Miller in good position to get a block on Chancellor, Hyde has a legitimate chance to turn up the sideline and get in the end zone here.

Maxwell might recover in time to get there and it’s possible Wright chases Hyde down as well. It might be wishful thinking, but I’ve seen Hyde run over enough people at the goal line that there’s no way I’m ruling out a score here.

For reasons I can’t possibly fathom, Kaepernick lofts a pass to the corner of the end zone for Miller. Considering Chancellor is in great position, I don’t love that throw if it’s intended for Boldin or Crabtree. Throwing it to the damn fullback should never be a consideration — the fact that Miller was able to occupy a defender was more than enough.

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Another Steven Hauschka field goal on Seattle’s ensuing possession extended the lead to 19–3, but it might as well have been 50–3. After failing to capitalize on numerous opportunities through the first three quarters, there was zero hope the 49ers’ offense would be able to move the ball well enough to produce the two or three scores needed to come back.

When all was said and done, Kaepernick didn’t complete a single one of his 10 throws that traveled more than 10 yards in the air. His 10.7 QBR and 1.07 adjusted yards per attempt were both the second-worst marks of his career. Football Outsiders’ defense-adjusted metrics didn’t like the game any more than the traditional numbers did. San Francisco’s minus–65.6 percent pass offense DVOA was their worst effort of the season by a considerable margin.

It’s important not to put too much stock into a single game. Kaepernick struggling against the Seahawks is nothing new; some of his worst games as a professional have come against Pete Carroll’s defense. But this game was different.

In previous games against Seattle, it was easy to point to factors outside of Kaepernick’s control as significant contributors to the offense’s poor showings. His cast of pass targets were mostly terrible (or missing) and appeared incapable of defeating the Seahawks’ press coverage. Pressure was an issue at times. And more than anything, Seattle’s defenders were just better.

That wasn’t the case in this game. Seattle’s press was rarely a problem as the 49ers used motion and various stacked and bunch alignments to allow their receivers free releases off the ball. Despite being sacked four times, Kaepernick was never really under consistent pressure. Plays were there against that defense, they just weren’t made.

This was the worst game I’ve ever seen Colin Kaepernick play.

Everything broke down with Kaepernick. He was wildly inaccurate for most of the night and constantly made poor decisions as to what to do with the football. I’ve spent more time watching Kaepernick than just about anyone. I’ve seen every single snap of his career, often a half-dozen times or more. I don’t mention this to imply that my opinion somehow holds more weight than everyone else’s, but rather to let you know that I don’t make this statement lightly… This was the worst game I’ve ever seen Colin Kaepernick play.

I don’t know what that means for the next four games or beyond. Probably nothing at all. It’s just one game. There’s still time for Kaepernick to iron out his inconsistencies. But it’s difficult not to think that we’re rapidly approaching the point where Kaepernick just is what he is: a quarterback capable of breathtaking highs and gut-punching lows. Unfortunately for the 49ers, this season has seen far more of the lows and they’ve left Jim Harbaugh’s team in danger of missing the postseason for the first time in his four seasons at the helm.