Brady was intercepted twice while the running backs lost two fumbles. Brady finished 36-of-65 for 443 yards, one touchdown and two interceptions, and a quarterback rating of 68.9.
It was a brutal first half for Brady and the offense, as he completed 10-of-19 passes for 76 yards and an interception. His quarterback rating at the half was 40.7.
But even down 31-3 with over 10 minutes left in the third quarter, Brady had a real sense the game wasn’t over.
“I didn’t think so,” Brady said when asked if he felt a sense of hopelessness. “I had a feeling we’d be able to come back. We hung in there, we battled back from a 28-point deficit, but we just made too many mistakes when we needed to make the plays. It’s a tough loss, but we’ve got to try to get some things corrected.”
Brady threw 46 passes in the second half and finished just shy of matching his boyhood idol Joe Montana  for the greatest comeback in regular season history. The 49ers erased a 35-7 deficit on Dec. 7, 1980 and won 38-35. Of course, the all-time comeback was when Buffalo wiped out a 35-3 hole and beat the Oilers, 41-38, in overtime in the 1993 playoffs.
Of course, many fans will point to and second-guess the decision to go for it on fourth-and-1 from New England’s own 12 with 2:24 left in the game, and still two timeouts and the two-minute warning at their disposal.
Did he think there might be any debate?
“No. I didn’t think about it,” Brady said. “We made a few of them. That was just bad execution.”
The Patriots converted their first three fourth-downs of the games before the incompletion on fourth-and-1. They finished 5-of-6 on fourth down but just 2-for-15 on third down, including 0-for-7 in the first half.
Here is the rest of Brady’s Q and A after the game:
Q: How shocked were you to only have three points at halftime? What were they doing to limit your powerful offense?
TB: Well, we were turning the ball over. It’s hard if you’re not making big plays and you can’t put together enough good plays to put together a scoring drive. And certainly to turn the ball over and give them a chance to score, which is pretty much what we did the entire first half. We just didn’t even give ourselves a chance. I mean, they’re a very good team and a very good defense and they play hard. We just spotted them 28 points. We fought hard, but you can’t play poorly against a good team and expect to win.
Q: Compared to what you were doing in the first half, how different was your offensive approach in the second half when you started to move the ball and score points?
TB: It was just execution. It wasn’t like there was a magic formula to what we were doing; we just stopped killing ourselves. We just can’t turn the ball over [and] we can’t miss plays that we have opportunities at. So, we hit a few of those and that’s why we moved the ball.
Q: Does your confidence get shaken when your younger backs put the ball on the ground like Shane Vereen  and Stevan Ridley did today? How do you proceed next week?
TB: Mental toughness. I think that’s what you show. It’s not every game is going to be perfect. Not every carry is going to be a 50-yard touchdown. Not every pass is going to be a 50-yard touchdown. It’s a matter of understanding what you need to do to help the team win and being selfless and doing your job. We did a better job of that in the second half; we just didn’t do a very good job in the first half.
Q: What about Brandon Lloyd ‘s performance tonight?
TB: Yeah, he played a great game. He played a great game and made some great catches when we needed it. He’s had two great weeks in a row and we’re going to need it down the stretch here. And certainly, the season isn’t over. We’ve got a lot of football to play. To play as poorly as we did tonight and still have an opportunity to win, we just have to do a better job.
Q: This loss changes the playoff scenarios a little bit. It’s going to be pretty tough for you guys to have home field advantage throughout like you normally do. Have you guys talked about that at all?
TB: We haven’t. You know, we haven’t thought about that yet. We’ve just been trying to string wins together and so forth. What’s in our control is winning football games. Certainly that was the goal tonight. It wasn’t the outcome, but that’s what we were trying to do. We put a lot into it. We knew the type of team we were playing.
We hung in there at times and there were times we didn’t. It’s unfortunate, but it’s OK. We’ve got two games left and certainly this game is very important to the outcome of our season, next week in Jacksonville.
Q: Do you think maybe the high of the Texans win carried over into practice and this week and maybe you weren’t focused enough on the 49ers?
TB: No, we were pretty focused on the 49ers. I think we understood what this team is all about and how good they were. We just didn’t play very well.
Q: How would you describe how they approached you guys defensively?
TB: I wouldn’t say it was a whole lot of different things. I think they do what they do and they do it very well. We made some mistakes early in the game and they capitalized. We couldn’t stay on the field on third down. [We] turned the ball over. I don’t know what our time of possession was, but I’m sure it wasn’t good. The first half was a terrible first half. We got down ‘ fortunately we were in it at the end of the first half, but we didn’t play well to start the second half. And then went on a little run, but you can’t play 30 minutes against a good team.
Q: When you’re getting beat schematically, you can make adjustments and change your approach. But how do you get over it when you’re beating yourselves?
TB: I think everyone just has to focus on possession of the ball. We have to focus on doing our job, the execution of the play. It’s not a matter of ‘Look, we’re going to call this special play and this is going to work out perfect and everyone is going to be wide open.’ No, I mean, what we did in the second half on the scoring drives, that’s what we have to do throughout the course of the game. And that’s what we’ve been doing; we just didn’t do it very well in the first half.