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SANTA CLARA, Calif. — It was looking really good when the sun was peeking out and the “Brady” chants were raining down at Levi’s Stadium Sunday afternoon.

It was looking pretty dismal when the actual drops rained down during the quarterback’s homecoming.

Playing through a steady downpour in front of a half-empty stadium – it’s possible Junipero Serra High had more fans at its state playoff win over Saint Francis Friday night — the Patriots survived a rock fight with the 49ers, earning a 30-17 victory.

It felt a lot closer than that.

Tom Brady completed 24 of 40 passes for 280 yards and 4 touchdowns in his first game in his backyard. By the end of the game, he might have been related to or had a close friendship with everyone left in the seats.

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The Patriots started and finished impressively but went through a stretch of five possessions through the middle quarters where they appeared to be stuck in neutral.

It wasn’t until the fourth quarter when the New England offense got back in gear, scoring 17 straight points to finally put this one in the win column.

“We started off great in the first quarter and then, you know, we did enough to win the game,’’ said Danny Amendola, the recipient of one of Brady’s two fourth-quarter TD passes. “They’re a good football team. They were flying around. They were ready to play today. We came out in the second half, made some adjustments and started connecting a little bit more.’’

Although the concern coming in was the defense, the normally high-octane offense raised some eyebrows and had some heads shaking as it struggled to move the ball against one of the league’s worst defenses.

James White is tripped up by Eric Reid in the second quarter.
James White is tripped up by Eric Reid in the second quarter.Matthew J. Lee/Globe staff

Brady led the Patriots to touchdowns on their first two possessions, throwing scoring strikes to Julian Edelman (4 yards) and James White (9 yards), and it appeared the rout was on. But the woeful 49ers (1-9) showed some fight as Colin Kaepernick marched them 92 yards on eight plays — firing an 18-yard TD to Vance McDonald to cut the Patriots’ lead to 13-10 at the half.

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It stayed that way through three quarters as neither team could do much in the wet conditions.

“We had good field position to start the game and on the two drives where we got it in. We had great field position and we took advantage of it,’’ said Brady. “We had some penalties that got us off track and they played some good defense. I wish we’d score every time, but they made it tough, too.’’

Brady showed off some fleet moves during the late surge, buying time in the pocket before connecting on both of his fourth-quarter TDs.

He hit Amendola with a 5-yard TD on the first play of the final stanza (capping a 10-play, 80-yard drive) and two possessions later hit Malcolm Mitchell with a 56-yard catch-and-run for the rookie’s first career TD.

Brady absorbed big hits as he delivered both scoring passes while on the run. “He’s Brady-Vick,’’ said Edelman with a laugh. “He’s a competitor. Nothing he does surprises me. He’s an unbelievable leader. Unbelievable football player. It’s an honor and pleasure to get to play with him.’’

Brady’s mobility definitely frustrated the 49ers.

“When you can extend plays like that, it’s definitely tough on the back end when the receivers are scrambling around,’’ said 49ers safety Antoine Bethea. “He has great awareness in the pocket . . . he did a great job today.’’

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Mitchell wasn’t surprised by the fight in the 49ers. In fact, he had a feeling it was going to be a grind despite the Patriots’ quick start.

“Football is a competitive sport. Great players on both sides of the ball,’’ said the rookie. “You have that tension going back and forth from time to time. That’s just normal.’’

Other observations as the Patriots moved to 8-2 with a Thanksgiving weekend date with the Jets on the horizon.

■  Patrick Chung continues to be a force. The rugged safety with the linebacker mentality finished with a game-high eight tackles on defense and another on special teams.

Despite his comparative lack of size (5 feet 11 inches, 215 pounds), Chung takes on all comers. He announced his presence early on, dropping Kaepernick for a 12-yard sack on the third play of the game.

LeGarrette Blount rushed for 124 yards Sunday.
LeGarrette Blount rushed for 124 yards Sunday.Matthew J. Lee/Globe staff

■  LeGarrette Blount keeps churning out yards.

It was a classic Blount kind of day as the beefy tailback rushed for 124 yards on 19 carries. His 6.5-yard average was helped greatly by his 44-yard scamper, and as usual, he did his beastly work in the late stages.

He carried 10 times for 80 yards in the second half as he helped kill the clock and the will of the 49ers defense.

“Every time you run a play you’re not going to score,’’ said Blount. “It takes drive. It takes consistency. That’s what we continue to do. We stay consistent and we stick to the game plan.’’

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■  The defense looked discombobulated early but rallied late.

New England used a lot of personnel changes in the first half and struggled to find consistency. Kaepernick was 8 of 9 for 116 yards and a TD over the first two periods and just 8 of 21 for 90 yards over the final 30 minutes.

Kaepernick, one of the more elusive quarterbacks in the league, was sacked five times, with Chung, Dont’a Hightower, Rob Ninkovich, Kyle Van Noy (first of his career), and Malcolm Butler (first of his career on the first play of the game) all getting one.


Jim McBride can reached at james.mcbride@globe.com. Follow him on Twitter @globejimmcbride.