The 3-0 Eagles steamed into brand new Levi’s Stadium, hoping to kick the 1-2 San Francisco 49ers while they were down (two key defenders out, the coach fighting with management, and Colin Kaepernick showing his flaws).

They left dismayed, perhaps exposed, with fans squabbling, coach Chip Kelly defensive and Nick Foles’s big contract payday at the end of this year in doubt.

That’s a lot of dismay for a team that came within two yards (on three consecutive plays) of a heroic, almost miraculous comeback that would have left them undefeated. But the way it happened was bizarre and troubling.

You see, the Eagles defense was strong, and the special teams were incredible. The punt return unit alone scored 14 points — a blocked punt for a touchdown, and a TD return by Darren Sproles. The defense was impressive, too. The Eagles’ much-maligned pass coverage was excellent, playing very tight and giving up only circus catches — plus one egregious rookie mistake.

Mark Saltveit

Marcus Smith II left his assigned man, RB Frank Gore, to chase Kaepernick on a scramble. Kaepernick threw a moon ball across his body to Gore — who had no one within 30 yards — for a touchdown. Aside from that one play, the Eagle defense was tight. The Birds even got the pass rush going, sacking Kaep four times (with two more sacks wiped away by penalty). So what’s the problem?

The offense, that’s what. You know, Chip Kelly’s specialty? That was leading the league, and scoring 30 points a game? They got zero points. Doodly squat. A goose egg. And that’s what was so discouraging.

LeSean McCoy — the NFL’s leading rusher last year — got 17 yards on 10 carries. He usually has a couple of individual carries with more yards than that per game. Foles was 21-43 passing, with two interceptions kept company by two fumbles.

Mark Saltveit

How could this happen? I see at least three major reasons.

First, credit San Francisco with an excellent game plan. Remember, Coach Harbaugh and defensive coordinator Vic Fangio faced off against Kelly when he was at Oregon, splitting two games in 2009 and 2010. (Oregon won both games when Kelly was just offensive coordinator, in 2007 and 2008.)

In fact, Chip told a reporter that he had visited with Harbaugh and Fangio after they went to the NFL, talking strategy. So they were well acquainted with his offense, and they attacked it in the most basic way possible.

Chip Kelly’s schemes rely heavily on counting the number of defenders in the box, which usually boils down to “how many safeties do you have? One or two?” As Sheil Kapadia explains in an excellent “dissection,” San Francisco showed two safeties, but often moved one (Antoine Bethea) up into the box right at the snap, while the other (Eric Reid) shifted to single high safety coverage. Other times they both stayed back. This made it very hard for Foles to make the correct decision. (Bethea had a tremendous game, by the way.)

Second, the Eagles’ wounded offensive line couldn’t fake it for yet another game. With Lane Johnson in the final game of his suspension for performance enhancing drugs, center Jason Kelce and guard Evan Mathis and even top sub Allen Barbre out injured, the crazy quilt front line was a mess. They were fair to middlin’ in pass protection, but fell down in the run game. Literally. Check out this run by McCoy, with 7:02 left in the second. (H/T to Sheil for finding it.)

On this outside zone play to the right, three of Philadelphia’s offensive linemen fall down — one tripping over another. The result is Shady with only Brent Celek blocking, versus six San Francisco tacklers.

from video (NFL Rewind)

LeSean can juke most defenders one on one. But this was more like trying to outrun a pack of dogs, with similar results.

from video (NFL Rewind)

Finally, I’m concerned that the Eagles are too tough for their own good, as I explored in an article at Bleeding Green Nation. What I mean is that we all love it when Brent Celek or Nick Foles or LeSean McCoy takes a brutal hit, and gets right back up and keeps playing. But maybe we shouldn’t be. We’re still learning about the effects of concussions.

None were officially diagnosed in these cases, but Celek took two helmet-removing shots in the preseason, and is 3 for 11 for 15 yards since then. (He averaged 15.7 yards per catch last year.) McCoy was speared helmet to helmet against Washington and has 29 yards on 27 carries since then. Foles has taken a lot of tough shots with the injured offensive line, and he has looked like he’s in a fog all year, not seeing open receivers and unable to judge distance on his long throws.

Clearly we can’t count on the league to protect players’ brains, or police helmet-led tackles of the sort that Washington was routinely laying down. But at least we as fans can think twice about cheering on the macho, “I didn’t feel that” attitude among players and make sure they’re not getting brain damage that cripples their lives as well as effectiveness on the field.

Edited by Torrey Drake

Feature photo by Mark Saltveit