(KPIX) — Stout defense and a dominant running game propelled the San Francisco 49ers through much of the regular season and playoffs. But with a 10-point lead over the Kansas City Chiefs after three quarters of Super Bowl LIV, those two things wouldn’t be enough. The Chiefs reeled off 21 unanswered points en route to a 31-20 win. And the 49ers were left wondering what hit them.

Up until the Kansas City run, the game had progressed about as well as San Francisco could’ve hoped. Patrick Mahomes had been limited to two scoring drives, yielding only 10 points. The play-calling, and the offense in general, seemed a little off. Some of that could’ve been the Chiefs’ tendency of late to start games slowly, and part of it could’ve been 49ers’ tenacious defense.

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The 49ers extended a 10-10 halftime tie to a 20-10 lead by the start of the fourth quarter. Fred Warner had intercepted a pass intended for Tyreek Hill to end the Chiefs’ first possession of the half. Three minutes into the fourth quarter, Tavarius Moore picked off another pass to Tyreek Hill to end the Chiefs’ second possession. Mahomes, who didn’t have a multiple-interception game all season, threw two in under 10 minutes.

Then it all seemed to fall apart. Mahomes, who seemed to lack answers up to that point, never lost his poise. He led three touchdown drives in quick succession, leaving the 49ers down by 11 points and stunned in the game’s waning minutes.

What happened to the defense? A seemingly fair question may also be the wrong question. “A lot of people are looking at the Niners defense, defensive coordinator but really, we have to talk about complimentary football,” according to former NFL wide receiver and Inside The NFL analyst Brandon Marshall. “It really started on the offensive side. On the offensive side, they should have run the ball more, controlled the clock better. And they didn’t, which put their defense in a tough spot.”

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A look at the 49ers’ second-half possessions confirms as much. Only the half-opening drive, which ended in a field goal and gave them the lead, took significant time off the clock. Their next possession, which extended their lead by a touchdown, only lasted 2:48. The following two possessions, both while still leading, lasted only 3:04 (five plays, 17 yards, punt) and 1:03 (three plays, five yards, punt).

The 49ers running game seems well designed to use time and hold on to a lead. But in the Super Bowl, they couldn’t when it mattered most. “It’s tough to really talk about the game after,” notes Marshall. “Why do you only run the ball 22 times? Well, if you look at what the Chiefs defense did, they were stout up front. They stuffed it. But, then you have to do other things. I think there were opportunities where they could have gotten a few more runs. But it was tough when you look at what that defensive line was able to do on the Chiefs side.”

So where does this leave a 49ers team that executed a miraculous season-over-season turnaround only to come up a little bit short? What do they do now?

“They just need to get back to work, get healthy,” says Marshall. “I think the biggest thing they need to do is recover mentally. Sometimes, when you lose a game like this, or win a game like this, this can last for another year or two. Look at the Philadelphia Eagles. They have been on this Super Bowl high for a couple of years now. So I think the Niners, the biggest thing they need to do this off-season is really regroup. If I’m coach Shanahan or John Lynch, that is what I’m focused on making sure our team recovers mentally as fast as possible so we can focus on next year.”

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You can catch Brandon Marshall along with Ray Lewis, Phil Simms and host James Brown when Inside The NFL airs tonight at 9 p.m. ET on Showtime.