PHILADELPHIA — For all the genius of Kyle Shanahan this season — all the mistakes, confidence, arrogance and winning — the NFL’s laws of averages suggested there had be a bottom to his quarterback bag. The only question was whether the San Francisco 49ers head coach could evade the moment, maybe outrun it, trick it or wizard it away and keep this improbable roll going.

But when the end finally came, the moment was as cruel as it was definitive.

Rookie third-stringer-turned-savior Brock Purdy couldn’t throw. Fourth-stringer Josh Johnson couldn’t play. Running back Christian McCaffrey was fitted with a quarterback wristband and the 49ers were down to two options: Keep Purdy in the game and let him hand the ball off, or use its marquee running back as the centerpiece in a Wildcat scheme. Either route, the Philadelphia Eagles had a monstrous defense that was leading 21-7 early in the third quarter of the NFC championship game and had the ultimate advantage over a Shanahan offense. Not only was it wholly one-dimensional with no functional passing quarterbacks left, but it also had no options left.

Suddenly, the Eagles had battered San Francisco’s depth chart into unseen territory this season. Two more quarterbacks had broken, leaving the bottom of Shanahan’s bag with nothing more than a fistful of air. It's the kind of thing that takes a legitimate Super Bowl contender and reduces it to a roster in collective disbelief, with players staring into the void of two more quarterback injuries and wondering what’s going on?

“I think everybody did [think] that,” 49ers tight end George Kittle said after Sunday’s lopsided 31-7 loss to the Eagles. “You dress two quarterbacks and neither one of them can throw and neither one of them is really available. It kind of limits what you can do as an offense.”

How limited? Kittle offered a finite number: 15 plays, give or take. With basically all of them featuring some kind of run element.

“You can only do so much,” Kittle said. “As soon as Purdy came back in, they put six guys on the line of scrimmage and they loaded the box. It’s not like we can do any play-actions or anything off it, so we just kind of had to run into it.”

This game was a massive Eagles story, of course. One in many, in fact. It was about a defense that has never gotten as much hype as it deserved and an edge rusher in Haason Reddick who is undoubtedly the most underrated game disrupter of the 2022 season. It was about a quarterback in Jalen Hurts who looks like he’s grinding through injury and a general manager in Howie Roseman who has masterfully reconstructed his second Super Bowl team with a different head coach and quarterback.

Those are the stories that will press forward the next two weeks into Super Bowl LVII. The 49ers ultimately won’t, undercutting one of the best defenses to fall short of the NFL’s biggest stage. Not to mention ending the storybook rookie season of Purdy, who went from the last pick in the 2022 NFL Draft to a legitimate contender to start for the franchise next season.

Perhaps it’s a remarkable testament to Purdy that the 49ers' offense faltered so badly in his absence, following a hit from Reddick on San Francisco’s first drive that ultimately forced a Purdy fumble and changed the game's trajectory. While the precise nature of the injury remained unknown Sunday night, it was serious enough to require an MRI this week. It's a reality that sounded apparent to the quarterback almost instantly, as he went to the sideline and told Shanahan the worst possible news: He couldn’t throw anymore.

“It just felt like really a lot of shocks all over from my elbow down to my wrist in [the] back [of my arm],” Purdy said. “Just pain, all over. … I told him right there [after the Reddick hit], ‘If we run a play, I can’t throw deep.’”

And that was it. With all due respect to journeyman Josh Johnson, the balance of momentum felt destined to slip as the game went on. Which it did, despite McCaffrey forging a 7-7 tie in the second quarter on a 23-yard TD run. It was a matter of only time before an elite Eagles defense imposed itself and turned the tables on a 49ers team that had been battering opponents all season long. Finally, when Johnson was lost early in the third quarter to a concussion — while trailing by 14 points — the only option left was to put Purdy and his clipped-throwing arm back into the game to hand off and hope for a miracle that never came close to materializing.

Just like that, the rookie quarterback who had commandeered San Francisco’s offense to a level worthy of a Super Bowl run was gone. And with him, Shanahan’s comfort with opening his entire playbook against a ferocious opponent. It was a moment that was one of the weirdest and likely one of the most disappointing in Shanahan’s history, taking its place next to a Super Bowl loss as an offensive coordinator with the Atlanta Falcons and then another as head coach of these 49ers. Neither of which felt as toothless as this one.

It was a visible bitterness as Shanahan walked off the field Sunday, with a clenched-jawed silence alongside his team. His eyes were steeled into a forward gaze, never acknowledging individuals around him who passed and offered subdued nods. They were the kind of exchanges you’d expect when a head coach makes three NFC title games in four years but still hasn’t managed to crack the calculus required to win a Super Bowl. A guy who will garner Coach of the Year votes and might even win the award for the first time in his career, largely for figuring a way out of quarterback messes all season long.

“Guys are pretty down in there,” Shanahan said after the loss. “We were really excited for today. … I wish we had a little bit better opportunity than we did today.”

Added Kittle, “How does that feel to lose an NFC championship game because I don’t have a quarterback? Pretty s*****, to be honest.”

For the most part, the one-sided nature of the loss will eliminate some of the second-guessing that could have occurred if the game had been closer. A 24-point defeat tends to numb questions about penalties, depth chart decisions and blocking schemes (like the one where tight end Tyler Kroft was attempting to block Reddick when the Purdy hit happened). At some point, the nature of injuries can bury a team and it’s fair to say that’s what happened to the 49ers' offense.

But that won’t eliminate the wondering about where this defense would have settled if Purdy hadn’t gotten hurt, or what this edition of the 49ers might have been capable of. It’s destined for change now, as all NFL teams are when their season ends — losing players and assistants coaches and front-office personnel. San Francisco will be no different, with the offseason turning to contracts and the future of defensive coordinator DeMeco Ryans. Not to mention the questions about how significant the injury is to Purdy’s arm and what that means for the future competition at the quarterback spot with Trey Lance.

Eventually, that will be the focus of this franchise. But only after it gets past the what-ifs: What if Purdy’s arm had survived Sunday’s hit? What if Jimmy Garoppolo had been healthy enough to step back into the backup spot? What if Johnson had gotten a real chance to see if Shanahan could engineer something with his fourth signal caller of the season? Eventually, the franchise will have to get over those questions, and the coaching staff and roster will need to step back onto this same trek again.

Kittle summed it Sunday night, speaking for a franchise that finally ran out of quarterback answers in the 2022 season.

“What-ifs just kind of litter our entire lives in a way, if we don’t achieve our goals,” he said. “I try not to look at what-if. S*** happened. How are you going to respond to it?”