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SANTA CLARA

The Mullens Magic finally ran out, but even then, Mullens himself didn’t really believe it.

With zeroes on the clock and the home team trailing at Levi’s Stadium on Monday night, the newest 49ers sensation chucked a desperation pass out the back of the end zone. But what was that? A flag on the turf. Mullens gestured to his bench eagerly and pointed toward the New York Giants defense, convinced the penalty was against the other guys.

“I thought there was a personal foul, but there wasn’t,” Mullens said after the game.

No, there wasn’t. It was a holding call on the 49ers. The Giants declined it. Game over. New York 27, San Francisco 23.

So Mullens, the toast of the league during the preceding week after engineering a 34-3 rout of the Raiders in his NFL debut, is now 1-1. He brought a delirious passer rating of 151.9 into the Giants game; it now stands at 88.3. In short, Nick Mullens fell to earth. He experienced his first real adversity as a professional quarterback, and the results were mixed.

On the negative side of the ledger, Mullens threw two interceptions, and the first one led directly to Giants points. Different 49ers had different perspectives on the giveaways.

“Neither of those picks were on him,” fullback Kyle Juszczyk said. “They were both tipped balls.”

But Juszczyk’s opinion is far outweighed by that of 49ers head coach Kyle Shanahan, and the latter wasn’t so forgiving. “I think he did some good things, and some things we need to improve on,” Shanahan said tersely when asked about Mullens.

Let’s run through those interceptions real quick. Both did indeed come on tipped passes, but that doesn’t mean Mullens should be absolved. The first came about 11 minutes into the game, with the 49ers up 3-0. Working deep in his own territory, the first-year quarterback threw an out route to Kendrick Bourne. It was a dangerous pass that could have turned into a pick six. Instead, Giants cornerback Janoris Jenkins got a hand on the ball and deflected it into the arms of linebacker B.J. Goodson.

“It wasn’t necessarily a terrible read,” Mullens said. “But it was late, and the corner made a good play on it. … I definitely would have it back.”

The second pick was harder to gauge. Mullens threw a pass behind Marquise Goodwin on a crossing route, and Goodwin, trying to adjust, inadvertently tipped it to, once again, Goodson. Goodwin had stopped on the route, then restarted. It looked like a mistake. Apparently, it was not.

“The route is a stop-and-start route, so I assume he did,” Shanahan said. “It looked like the ball was a little bit behind him. I’d love Nick to throw a better ball, and I expect Marquis to catch that regardless.”

I think we can all agree that interceptions are bad, and that the two Mullens threw were a big factor in the 49ers’ loss. But I was surprised to hear the edge in Shanahan’s voice when he talked about Mullens. Because for a guy making his second NFL start, he generally looked pretty good.

Here are Mullens’ numbers against New York: 27 of 39 for 250 yards and a touchdown, along with the two picks. The 49ers had 374 yards of offense. It was a case of crisp efficiency, done in by a pair of turnovers.

Yes, that’s a mixed bag, but did you watch C.J. Beathard during his five starts? Bless his heart, but that was not a mixed bag. That was a bag of candy corn, the Halloween treat no one wants.

Beathard has the courage of a gladiator. He stands in the pocket and takes a beating and never complains, never stops fighting. But his throws are scattershot, and when he is under center, the 49ers’ offense rarely gets into any sustained groove.

Ignore Mullens’ interceptions for a moment, if you can, and look at the rhythm in which he plays. He checks down to secondary receivers. He gets the ball out of his hand quickly — one reason he has yet to be sacked, while Beathard was dumped 18 times in his five starts. And he hits receivers in stride. Mullens does not have a particularly strong arm, which is why the deep out will always be a difficult throw for him. But he is a pleasure to watch when he’s firing those slants and crossing routes to Goodwin and tight end George Kittle.

Look, I know Mullens has limitations. But this isn’t Montana vs. Young we’re talking about. It’s the competition for No. 2 quarterback next year when Jimmy Garoppolo has mended the ligaments in his knee.

This was a big game for Mullens. Everything went right for him against the uninterested Raiders on that Thursday night. Granted, Mullens was a big reason it all went so smoothly. But you knew not every game would be like that. There would be trials. How would he react?

We found out Monday, after that first interception helped give the Giants a 7-3 lead.

“We were all interested to see how he would respond against some adversity,” Juszczyk said. “And I thought he did so. He had some nice third-down conversions. He had some plays where he stepped into the throw while he was still getting hit. You respect that, and you love to see that from your quarterback.”

As Goodwin put it: “He didn’t flinch at all.”

Particularly encouraging was the 49ers’ final drive, though it ended in failure. They got the ball on their 25-yard line with 53 seconds left, needing a touchdown. The possession began with the Giants’ Lorenzo Carter drilling Mullens on a blitz — and getting called for roughing the passer. Mullens then completed three passes for 44 yards to three different receivers, managing to spike the ball with 1 second left to give him and his offense a final chance at the end zone. They didn’t get there, but the effort was solid.

“That’s why it hurts so bad, man,” Mullens said. “I really had fun out there. Thought we really worked well together. We just didn’t score enough points.”

Now the 49ers go into a bye week. They return with a game at Tampa Bay on Nov. 25. And the starting quarterback will be … who? Shanahan wasn’t prepared to show his hand.

“I haven’t thought about it yet,” he said.

But what’s to think about? Mullens might not be magic anymore, but he clearly has played better than Beathard this season. Tell the kid he’s the starter and give him some extra time to prepare for the Buccaneers.

You can reach columnist Phil Barber at 707-521-5263 or phil.barber@pressdemocrat.com. Follow him on Twitter: @Skinny_Post.

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