NEW ORLEANS -- Here's something no one saw coming when San Francisco coach Jim Harbaugh named untested Colin Kaepernick his starting quarterback ahead of Alex Smith in late November: As the 49ers prepare for Baltimore in the Super Bowl, their defense has more question marks than Kaepernick.
Kaepernick answered any lingering doubts about Harbaugh's unconventional decision with his performance in the NFC playoffs. He ran for 181 yards as San Francisco outscored Green Bay 45-31 in the divisional round, shattering the NFL postseason record for rushing yards by a quarterback. He had only two carries against Atlanta in the NFC championship game, but he completed 16 of 21 passes for 233 yards and rallied the 49ers to a 28-24 victory from a 17-0 deficit.
The Baltimore Ravens won't know what to expect from him Sunday in the Superdome.
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“Colin's play has been outstanding,” Harbaugh said. “He deserves a tremendous amount of credit for that.”
It's hard to know what to expect from the 49ers' defense, too. A physical, intimidating group for most of the last two years, it has dropped off significantly down the stretch.
The slippage started when All-Pro defensive end Justin Smith sustained a partially torn triceps tendon in the third quarter against New England on Dec. 16. The 49ers, who were dominating the Patriots 31-3, blew that lead in less than 15 minutes before escaping with a 41-34 win. New England rolled up 520 yards, the most San Francisco has allowed in Harbaugh's two years.
Smith sat out the following week as Seattle trounced San Francisco 42-13. The Seahawks' Russell Wilson threw four TD passes and Marshawn Lynch rushed for 112 yards.
Smith returned for the playoffs, but the defense has not regained its early season form. After a decent but hardly dominant performance against Green Bay, the 49ers gave up 477 yards to Atlanta and barely held on in the final minute.
The No. 1 concern is Smith's gimpy left arm, which requires a brace and has limited his effectiveness. When he is healthy, he helps shut down the run -- San Francisco allowed only 3.7 yards per carry in the regular season -- and gives pass-rushing linebacker Aldon Smith the freedom to torment quarterbacks.
None of Aldon Smith's NFC-leading 19½ sacks have come since Justin Smith's injury.
“You try to do as much as you normally do as far as technique and the way you're shedding blocks, but there's a limited range of motion, sure,” Justin Smith said. “It's getting better every week. I'm getting used to wearing the brace a little bit better, and I know how many games we have left now. Four more quarters.”
The 49ers allowed 30 or more points once in their first 31 games under Harbaugh. It's happened three times in the last five, and the Falcons came within 10 yards of making it four out of five Jan 20.
“We're here, [in the Super Bowl],” Justin Smith said. “I'm not going to get into a breakdown of how we played, but we obviously can play better. The other guys on the other side get paid, too. [Matt] Ryan and [Aaron] Rodgers are going to give you trouble.”
With Aldon Smith going sackless, the 49ers' secondary gave up nine touchdown passes to Russell, Rodgers and Ryan. That trio completed 68.6 percent of its throws.
This, from a defense that held five of its first 10 opponents to seven points or fewer.
Still, the 49ers don't sound concerned. They don't think their defense has dropped off as much as the numbers indicate.
“The teams we've faced have done a good job of finding some things that cost us a little bit,” safety Dashon Goldson said. “I give them credit, but overall we've played well as a defense and a secondary.”