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Tom Brady threw just in time to find Malcolm Mitchell for a 56-yard touchdown.
Tom Brady threw just in time to find Malcolm Mitchell for a 56-yard touchdown.MATTHEW J. LEE/GLOBE STAFF

SANTA CLARA, Calif. — Everyone at Levi’s Stadium on Sunday knew they were coming to watch a running quarterback.

Few expected that running quarterback to be Tom Brady, not Colin Kaepernick.

Brady showed off those crazy legs in Sunday’s 30-17 homecoming win over the 49ers, using his feet to avoid the pass rush, buy time, and find his second and third options down the field.

Brady’s feet helped break open a surprisingly tight game that was 13-10 entering the fourth quarter. He avoided the rush and improvised on a 5-yard touchdown pass to Danny Amendola that put the Patriots ahead by 10 points, then did it again on a 56-yard touchdown pass to Malcolm Mitchell with 10:06 left that put the game out of reach.

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“We’ve seen him do that before,” Bill Belichick said of his mobile quarterback. “It’s what good quarterbacks do — they have good vision, they know when they don’t have it. Our receivers did a good job of finding space, Tom did a good job of finding them, the protection did a good job of giving him enough time to get his eyes downfield and find a secondary target.”

Playing in a downpour for most of the game, and playing without star tight end Rob Gronkowski and trusty receiver Chris Hogan, Brady was 24 of 40 for 280 yards, four touchdowns, and no interceptions while playing in front of family and friends.

And after struggling to move the ball in the first half, Brady put the Patriots on his back — and his feet — in the second half. Brady’s splits: 12 of 17 for 108 yards and two touchdowns in the first half, and 12 of 23 for 172 yards and two touchdowns in the second half.

The Patriots’ final rushing numbers looked great — 30 carries for 171 yards, a 5.7-yard average — but they had a tough go at it through much of the second and third quarters, when the 49ers brought extra defenders to the line of scrimmage.

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That forced the Patriots to put the ball in Brady’s hands, and he delivered.

“It wasn’t a great day to throw the ball,” Belichick said. “San Francisco did a good job of coming down, crowding the line of scrimmage. They had a safety in the box, they had us outnumbered on almost every play. It was hard to just run the ball against the eight- and nine-man fronts that they were presenting.”

Brady has become a health and fitness nut in recent years, and he moves around better at 39 than he did at 29. He credits his resistance training with body coach Alex Guerrero for helping improve his mobility.

Brady rushed four times for 12 yards, though one was a kneeldown at the end of the game. He had a 7-yard rush on second and 10 in the first quarter, and later picked up a first down with a 3-yard scramble.

He’ll never be confused with Michael Vick, but Brady’s running stats are noticeably better this year. He’s averaging three attempts per game, only the second time in his 17-year career that he has reached that number. His 10.5 rushing yards per game represent a career high. And he’s averaging more than one first down per game with his feet, only the third time in his career he has done so.

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“I’m trying not to do that, truthfully,” Brady said of his rushing stats. “They were pretty good in coverage today, they took away some of those early reads and then held onto it. But there’s a lot of opportunities to be made when you do that because our guys can spring free with their quickness.”

And spring free they did in the fourth quarter, turning a close game into a blowout. Early in the fourth quarter, Brady spun out of the grasp of one pass rusher, reset his feet, and lofted a pass to Amendola in the back of the end zone while sliding down and taking a hit from another defender.

Brady credited Amendola for getting open.

“We got a little different coverage than we wanted and I had to buy a little bit more time and Danny made a great play finding some space,” Brady said. “I just kind of threw it up there for him, but that was a great play by Danny.”

But Belichick gave Brady his due.

“That’s a tremendous play,” the coach said.

A few minutes later in the fourth quarter, Brady avoided the rush, stepped up in the pocket, and got hit from behind as he threw on the run. But he found Mitchell in stride, who raced past three defenders for a back-breaking 56-yard touchdown.

Tom Brady delivered Malcolm Mitchell’s first NFL touchdown reception in the fourth quarter.
Tom Brady delivered Malcolm Mitchell’s first NFL touchdown reception in the fourth quarter.Matthew J. Lee/Globe staf

Brady, again, gave Mitchell the credit for the play.

“He was short of the sticks, then I scrambled up, he wheeled, and I just saw him, saw a little separation, just tried to give him a chance,” Brady said. “He made a great play. That was a phenomenal play by Malcolm. We really needed it.”

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Brady didn’t even realize he got hit on the play.

“Someone said, ‘You got hit on that,’ but I don’t remember that,” Brady said. “You throw it and you see it on the film the next day.”

Brady said he prefers sticking to the script, but he’s been working hard on his mobility for instances like Sunday, when the defense is taking away initial reads and Brady is forced to improvise.

“You prefer the play just to play out like you would hope, and when it doesn’t you got to make some improvisational ones,” Brady said. “And our guys made some really great plays today.”

None better than from Brady himself.


Ben Volin can be reached at ben.volin@globe.com. Follow him on Twitter @BenVolin.