49ers John Lynch and Kyle Shanahan built ‘great equalizer’ for Super Bowl moments like this. Will it be enough vs. Patrick Mahomes?

(Bruno Rouby/Yahoo Sports)

John Lynch told the story the last time this happened.

When the San Francisco 49ers and Kansas City Chiefs faced off in a Super Bowl just four years ago, the 49ers general manager faced the same concern.

How do you stop Patrick Mahomes?

Lynch thought back to his January 2017 interview with the 49ers, and the exercise that management gave their now-general manager and head coach.

You have 150 points in your salary cap. How are you allocating resources?

Lynch and head coach Kyle Shanahan performed the exercise separately. And yet … “It’s been communicated to me that [we] were almost directly in sync,” Lynch said. “Maybe they hired us for that reason.”

The synchronicity wasn’t a given: Lynch was a Hall of Fame safety in his playing days, while Shahanan grew up the son of a two-time Super Bowl-winning head coach whose offensive philosophies continue to shape the NFL. But when each thought about offense, Shanahan from the standpoint of what frustrated his schematic potential and Lynch from the standpoint of what enabled his career to thrive, they landed on common ground: Invest “a lot” in the defensive line.

“We talked about quarterback, and then you’ve got to find the guys to knock him down,” Lynch said before the Super Bowl four years ago. “When you’re playing an offense like [the Chiefs], when you’re playing a quarterback like Mahomes, I think it can be the great equalizer.”

To triumph Sunday, the 49ers need it to be.

Will it?

SANTA CLARA, CA - MAY 12: Head Coach Kyle Shanahan and General Manager John Lynch of the San Francisco 49ers during rookie training camp at the SAP Performance Facility on May 12, 2023 in Santa Clara, California.  (Photo by Michael Zagaris/San Francisco 49ers/Getty Images)
Head coach Kyle Shanahan, left, and general manager John Lynch are getting their second shot at a Super Bowl title. (Photo by Michael Zagaris/San Francisco 49ers/Getty Images) (Michael Zagaris via Getty Images)

49ers need well-resourced defensive front to step up consistency

San Francisco’s offense has been routinely lethal this season. The 49ers ranked first in offensive DVOA, third in points scored and second in yardage. Their raw regular-season defensive numbers were similarly strong: fourth in defensive DVOA, third in points allowed and eighth in yards allowed.

But inside the building, the 49ers know the front seven on which they depend has struggled.

“We had some spurts where we did it well and then we showed some where we’re inconsistent,” defensive coordinator Steve Wilks said. “It’s just really about trying to pull the trigger … not anything dealing with the scheme. It’s just that individual ready to go make a play and just got to pull the trigger.”

Getting opponents off the field has been a challenge.

Across the regular season, the 49ers ranked bottom-10 (24th) allowing third-down conversions on 40.93% of attempts. In each of their postseason games, that mark was worse: The Green Bay Packers converted on 53.9% of 13 third-down attempts while the Detroit Lions converted on 50% of their 12.

“Particular plays,” Wilks said, weren’t “to our standard. Those guys understand and know that and quite honestly it was embarrassing.”

SANTA CLARA, CA - JANUARY 28: Nick Bosa #97 of the San Francisco 49ers sacks Jared Goff #16 of the Detroit Lions during the NFC Championship game at Levi's Stadium on January 28, 2024 in Santa Clara, California. The 49ers defeated the Lions 34-31. (Photo by Michael Zagaris/San Francisco 49ers/Getty Images)

Niners brass’ high expectations stem from high investment that has not yet panned out. By their last Super Bowl stage, the 49ers had already invested a handful of first-round draft capital into their defensive line. They’ve since diversified their acquisition methods to feature premium free-agent targets and pricey extensions.

Arik Armstead, who started at defensive end for the 49ers four years ago but has since moved inside, received his five-year, $85 million extension a month after the last big game. If that sounds hefty, sit down before you consider that the Niners signed their second overall pick of the 2019 draft to a five-year, $170 million extension entering this season.

Nick Bosa’s price tag extended negotiations but didn’t derail them. “That hotline’s closed,” Lynch said in April. “That never opened.”

The duo that will start their second Super Bowl for the San Francisco defensive line now pairs with two other players upon whom the 49ers did not stumble passively. San Francisco signed defensive tackle Javon Hargrave last free agency when his price tag surpassed what the Philadelphia Eagles were comfortable with; they acquired defensive end Chase Young from the Washington Commanders at the trade deadline for a third-round draft pick, even though a mere half season remained on Young’s rookie contract. The acquisition paired Bosa not only with a former college teammate but also with another No. 2 overall pick.

Investments like those were made for moments like these.

“I think the quarterback is as hard to beat as anyone who’s ever played the game,” Shanahan said of Mahomes. “The things he can do from a talent standpoint and then you pair that up with his scheme with Andy [Reid]?

“They always have a chance.”

Mahomes, Travis Kelce toughest test for 49ers' front 7

A month ago, Mahomes’ ceiling seemed otherworldly while his floor — and often his reality — seemed average. Whether due to coordinator change, his own health and techniques or (most likely) his set of receivers, Mahomes dropped from second in passer rating to 14th; his touchdown-to-interception ratio slipped from last season's 3.41 (41:12) to this year’s 1.93 (27:14). But Mahomes enters the Super Bowl riding a four-game streak without an interception. He has not turned the ball over in the postseason, and he has reestablished his dominant rapport with tight end Travis Kelce, who’s averaged 87.3 yards and a touchdown per game after a regular-season mark of 65.6 per game and a score every three.

Add in a Chiefs scheme that will aim to disrupt the 49ers’ timing within bunch and stack formations, further deceiving with motion, and San Francisco expects to encounter improvisation.

“When they start to ad-lib, we’ve got to do a great job of really plastering the man within our zone and really straining to make sure we finish the rep,” Wilks said of Mahomes and Kelce. “It’s two plays within one down: When the ball snaps and then once [Mahomes] starts to scramble. So he’s phenomenal.

“The best I’ve ever seen for just buying time, winning with his feet and getting the ball where it needs to go down the field.”

The need to extinguish such a spark doesn’t surprise Lynch and Shahanan, who knew from the time they were candidates for these jobs that they’d need that great equalizer. But after a stout defense failed to thwart Mahomes four years ago, losing 31-20, questions over how much has changed — or better yet, how much the production has changed when the personnel has evolved — linger.

Have Lynch and Shanahan allocated enough of their 150 points, and the right ones?

The 49ers will soon find out whether they’ve found their great equalizer.