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49ers’ run defense spoils Kaepernick’s return in 45-16 loss to Buffalo

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Colin Kaepernick’s solid 2016 debut was spoiled by the 49ers’ suspect run defense in a 45-16 loss to the Buffalo Bills.

San Francisco pathetically allowed 312 yards on the ground, the most they’ve allowed in one game since 1972. It’s the fifth consecutive week they’ve allowed a 100-yard rusher. This time it was LeSean McCoy who galloped for 140 yards and three touchdowns. The 49ers are the worst run defense in the NFL and they will pick in the top three of the NFL Draft because of this fatal flaw.

To the surprise of many, Kaepernick moved the football throughout the afternoon and led three scoring drives in the first half. A 53-yard touchdown bomb to Torrey Smith in the second quarter reminded the NFL that Kaepernick is still capable of big plays. Kaepernick struggled in the second half, though. He finished with 13-for-29, 187 yards, one touchdown, no interceptions and eight carries for 66 yards. The bottom line: No quarterback could’ve overcome the 49ers’ awful run defense.

Chip Kelly will regret taking the ball out of Kaepernick’s hands late in the third quarter. On 4th and 2 inside Buffalo’s territory, Kelly called a draw play to Mike Davis which was stuffed at the line of scrimmage. Four plays later, Tyrod Taylor launched a 30-yard touchdown strike to Justin Hunter, beating both Eric Reid and Antoine Bethea in the corner of the end zone.

The Bills took a 24-13 lead and started piling on late in a blowout loss. McCoy would add a 30-yard touchdown run early in the fourth quarter, the 49ers would fumble the ensuing kickoff, and the Taylor launched the very next play for a 17-yard touchdown to Robert Woods. To add insult to injury, backup running back Mike Gillislee peeled off a 44-yard touchdown scamper, the final touchdown to cap a bloodbath of a second half.

On the positive side, Arik Armstead had his most active game of the year. The second-year defensive end jumped the snap in the first quarter, leveling Taylor and forcing a fumble. Rookie teammate DeForest Buckner recovered the fumble and the 49ers kicked a field goal shortly after. Keith Reaser had a strong game after replacing the injured Rashard Robinson.

But despite a few big plays, the defensive performance was completely unacceptable. The unit was supposed to show signs of growth in 2016, and instead, have become one of the NFL’s laughingstocks. Remember this: the run defense was already struggling before NaVorro Bowman tore his Achilles. Now defensive coordinator Jim O’Neil’s unit looks damaged beyond repair.