FOXBORO -- Brian Waters is smart. He’s also been around the league for a few years. So even though he’s only been in New England since the summer, when Sunday’s game between the Patriots and the Colts ended, he knew what his team was in for.

“We definitely didn’t finish the way we wanted to finish. I’m sure that’s something that’s going to be really emphasized this week,” Waters said with a rueful smile following the game.

“I haven’t been here long time, but I’ve been here long enough to know when certain things will be a point of emphasis.”

In Sunday’s win 31-24 win over the Colts (click here for the complete recap), the Patriots were able to put together 45 good minutes of football, pushing out to a 31-3 lead and generally making people forget about the idea of Indianapolis even managing to threaten New England.

But all that good feeling came to an end in the fourth quarter. The Patriots offense had 11 yards of total offense in the quarter (they were 0-for-3 on third down and did not pick up a first down). Meanwhile, the Colts had 21 points in the fourth quarter, the most New England had yielded in the fourth all season long.

Whether it was scheme (namely, a willingness to trade points for big chunks of clock) or personnel (New England made several wholesale substitutions on both sides of the ball throughout the quarter), the Colts suddenly made it a one-score game with less than a minute to go. And while the Patriots recovered the final onside kick to allow themselves to secure a win, they still couldn’t shake the overall feeling of dread that permeated some corner of the New England locker room.

“We played good for 45 minutes, and then didn’t do anything offensively in the fourth quarter,” quarterback Tom Brady said after the game. “So we’ll hear about that [Monday].”

“We just know that in the end, as a team, we have the talent and we have the mentality, we just have to finish strong,” said defensive end Andre Carter. “It’s something that we have to communicate as a group and as a team, and move on from there.”

“I think in general it’s a mindset. It’s just knowing what you have to do and going out there trying to execute. Unfortunately, towards the end, final stretch of the game, Indy was just able to make big plays and that is something we have to eliminate.”

Needless to say, the Patriots did not get Monday off from Patriots coach Bill Belichick. In fact, they’re probably in for a long day of film study, with a specific focus on the fourth quarter. That means Monday ... well, Monday is going to be rough.

“Look, I don’t think you’re ever going to take a win for granted. That’s for sure. I do realize that we have ... not to say we have bigger picture-type dreams, but you really want to make sure you’re playing a better brand of football,” Waters said. “The focus is on going forward, down the stretch, to make sure we’re playing 60 minutes of good football, every game. And today wasn’t that.”

This is not to say that the Patriots aren’t going to give the win back. As they reminded us several times over the last week, it’s hard to win games in the NFL, and each time you do, it should be celebrated. The fact remains that the Patriots are 9-3. They remain in the drivers’ seat when it comes to clinching one of the top two seeds in the AFC, especially when you consider their schedule down the stretch.

Maybe with those facts in mind, Waters ended things on an optimistic note.

“Now, I’m still going to be happy. I’m still glad we won the football game. Other people may have different feelings about it, but I’m glad we won and I’ll be prepared for whatever we have coming in here next week. That’s the sign of a good football team -- the guys who can come back after a win, loss, tough win, tough loss, whatever it may be, and come back and get prepared the same way. I expect that preparation to be as high as it has been at any point in the season.”

Here are nine other things we learned Sunday at Gillette Stadium:

WHILE HIS PERENNIAL COUNTERPOINT WATCHED FROM THE SIDELINES, TOM BRADY PUT TOGETHER TWO GREAT QUARTERS OF FOOTBALL

For so many years, Patriots-Colts was defined by Tom Brady and Peyton Manning. On Sunday, Manning made the trip to Foxboro, but remained on the sidelines because of the neck injury that has kept him out all season long. Meanwhile, Brady and the rest of the New England offense struggled for the first quarter, but he was at his tactical best in the second and third quarters when he engineered four touchdown drives that averaged 10 plays and 73 yards each, including a 16-play 86-yarder in the second quarter that took 6:40 and gave the Patriots the lead for good. Brady appears to be over whatever elbow/consistency issues that slowed him down earlier this season, as he threw for at least 290 yards, hit Rob Gronkowski with a pair of touchdown passes (for more on Gronkowski's performance, check out Kirk Minihane's column here)  and had a completion percentage better than 66 percent for the third time in the last four games. (For what it’s worth, he’s now got a four-game streak where he hasn’t thrown a pick -- his longest stretch since last season.)

By the numbers: With two touchdown passes on Sunday, Brady passed Johnny Unitas and moved into a tie with Warren Moon for sixth on the NFL’s all-time touchdown pass list. Brady’s 11-yard touchdown pass to Gronkowski in the second quarter was his 290th career touchdown pass, tying Johnny Unitas for seventh place on the NFL’s all-time list. He completed a 21-yard touchdown pass to Gronkowski to move past Unitas into a tie for sixth place with Warren Moon at 291 career touchdown passes. John Elway is in fifth with 300.

Money quote: “As a defense, they pretty much had the same guys out there that they had last year. They have a great pass rush. I thought we could execute better at times, but I’m glad we won and we have to move on.” -- Brady on Sunday’s performance.

THE PATRIOTS RUNNING GAME NEVER SEEMED TO GET ON TRACK

Whether it was scheme or playcalling or subpar blocking, the New England run game was unable to shake off a slow start (33 yards in the first half) against the 31st run defense in the league, and never managed to make a dent in the Indianapolis defense, ending with 73 yards on 24 carries. (It was the third-lowest output for the season for the New England running game, trailing only the 43 yards the Patriots had in the October loss to Pittsburgh and the 60 they had last month in the win over the Jets.) The Patriots got 33 yards on eight carries from rookie Steven Ridley, 14 yards on six carries from BenJarvus Green-Ellis and 12 carries on four yards from Danny Woodhead. (They were the only three in double figures in rushing yardage.) For Green-Ellis, it was his third-worst rushing output of the season, trailing only a nine-yard outing against the Steelers and an eight-yard outing against the Jets in the previously mentioned contests.

By the numbers: The highlight of the afternoon for the New England running game came when Green-Ellis punched one in from one yard out with 13 seconds left in the first half to give the Patriots a 17-3 lead just before halftime. The Patriots are now 20-1 (.952) when Green-Ellis has a rushing touchdown in a game. (The only Patriots loss was a 2008 game at Indianapolis.)

Money quote:  “The middle part of the game was awesome. We just came up third, fourth and a quarter of a yard short on the one and never got out of the long yardage situation there in the second to last drive. We’ll try to do a better job of that next week.” -- Brady on the New England offense on Sunday.

THAT BEING SAID, IT WAS A GOOD DAY FOR THE OFFENSIVE LINE

The Patriots offensive line had been battered over the previous two weeks, but against the Colts, they were very sturdy, allowing one sack of zero yards of the quarterback. While Indianapolis was able to occasionally get pressure up the middle, the New England tackles (Matt Light and Nate Solder) were able to hold pass-rushing terrors Dwight Freeney and Robert Mathis without a sack, while Mathis had just one quarterback hit. (As a team, the Colts were able to get four quarterback hits on Brady.) With the extra time, Brady was able to go 29-for-38 for 293 yards and two touchdowns.

By the numbers: Brady was sacked once on Sunday, and has now been sacked 21 times this season. He’s on pace for 28 sacks for the regular-season, which would be the most since he was sacked 32 times in 2003. (His career-high is 41 sacks in 2001.)

Money quote: “The guys are not taking anything for granted. Like I said, you never know when your number is going to be called, and the fact that when these guys are prepared and performing as well as they are so far is a true credit to not only how coach Scar coaches us, but it’s a true credit to those young guys understanding that when you come in this locker room, you better be prepared. You have to be ready to go when your number is called.”  -- Waters on the fact that there are now several moving parts on the New England offensive line.

THE NO HUDDLE REMAINS ONE OF THE PATRIOTS’ BEST OFFENSIVE WEAPONS

Over the course of the 2011 season, the Patriots have been able to be effective in the no-huddle offense. On Sunday against the Colts, they used it to jump start their offense at the end of the second quarter and the start of the third. Locked in a three-all duel with Indy, the went no huddle for the first time midway through the second quarter, and used it five times on a 16-play drive that ended with a pass from Brady to Gronkowski. On their final drive of the first half, the Patriots used it four times on an eight-play drive that also ended with a score. The same was true on New England’s two touchdown drives in the fourth quarter (six plays on a seven-play drive and six plays on a nine-play drive). The Patriots used it sparingly in the fourth quarter, but by that point, the game was 31-3.

By the numbers: The Patriots were in the no huddle for 24 plays from scrimmage on Sunday, and gained 195 yards on no-huddle plays, averaging 8.125 yards per play. For the game, New England averaged 5.8 yards per play.

Money quote: “If we’re not executing plays and just running the no huddle, we’re going three and out. The thing is to make sure that we’re executing our plays when we do get into that type of situation. We did seem to do a good job with that today. ... We like running it, but the guys want to make sure we’re doing the right thing. Taking our time and doing exactly what we need to do to make sure we’re getting positive plays.”  -- Deion Branch on some of the challenges faced by the Patriots when they run the no-huddle offense.

VERY QUIETLY, WES WELKER HAD ONE OF THE MOST IMPRESSIVE GAMES OF THE SEASON

It’s almost hard to believe, but Welker finished with a remarkable 11 catches for 114 yards Sunday against the Colts. There was no flash to the yards that Welker was able to pile up on Sunday (his longest catch went for 18 yards). Instead, it was grind it out yardage over the middle. Indianapolis decided to mix up coverages, going with more zone than man, but in the end, it didn’t matter, as he was able to get free release off the line much of the afternoon, and making the Colts pay as a result. He was at his best in the second quarter, when he compiled 62 of his receiving yards, including a total of 27 yards on New England’s final drive of the first half (an eight-play, 64-yard series that ended with a one-yard plunge from BenJarvus Green-Ellis with 18 seconds left in the quarter). With 82 catches for 1,143 receiving yards through 12 games, he’s now on pace for 109 catches and 1,524 receiving yards. He’s fallen off the record pace he was setting earlier in the season, but for someone in a contract season, it’s still an impressive performance.

By the numbers: Welker was targeted 11 times and had 11 receptions. It was the first time this season that a New England receiver was targeted at least 10 times and came away with all 10 receptions.

Money quote: “I think they had some injury issues with their DBs and things like that. We were able to kind of take advantage of going fast and have them line up in a lot of zone. They were kind of trying to get lined up more than anything. We didn’t see very much man. It was a matter of our spacing and Tom [Brady] finding the open guy and moving the ball down the field that way.” -- Welker on the Indianapolis secondary.

NICK MCDONALD WASN’T NOTICED

Earlier in the week, Belichick was trying to explain why Ryan Wendell had done such a good job as an offensive lineman, and said that it’s good when you don’t necessarily notice that someone different is in there. That certainly appeared to be the case with Nick McDonald on Sunday against the Colts, who stepped in for Wendell, who was hobbled with a calf injury this week. The Patriots were able to get good pass protection for Brady, and while there were some problems in the running game (the Patriots only had 73 rushing yards against the league’s 31st run defense), it was a solid debut for McDonald.

By the numbers: On Sunday, the Patriots started their fourth different center of the season in McDonald.

Money quote:  “I felt great. It’s always been a dream of mine to be out there with the starters. I felt real good. ... No, everything felt good. Obviously, I have some things to clean up, you know being my first game out there. I’ve just got to keep improving.” -- McDonald on his first NFL start.

JEROD MAYO DOES HAVE PLAYMAKING ABILITIES

The linebacker produced the most impressive interception of the season late in the game -- the unquestioned high point of the fourth quarter for the Patriots -- when he dove for an interception of Orlovsky while in zone coverage, coming away with the first interception of his career. The linebacker read the eyes of the quarterback and snatched the ball out of midair. It was a tremendous play, mixing Mayo’s football smarts with his athletic abilities. In addition, the linebacker was able to tip an Orlovsky pass that was intended for Indy tight end Jacob Tamme in the end zone, knocking the ball incomplete.

By the numbers: Mayo had the most complete day of any of the New England defenders, at least according to the stat sheet. He had seven tackles (two solo), to go along with two quarterback hits, his interception and two passes defensed.

Money quote: “It’s kind of disappointing to be honest with you. Even though it’s a win and it’s hard to win games in the National Football League, at the same time, you want to finish so much stronger than that.” -- Mayo on the performance of the New England defense down the stretch against the Colts.

THE DEFENSIVE LINE HAD A VERY GOOD AFTERNOON

The Patriots did some shuffling up front, but mainly utilized a rotation of Andre Carter, Kyle Love and Vince Wilfork, with Rob Ninkovich occasionally lining up with his hand on the ground as an extra defensive lineman. They were to do a very good job of bottling up the Indianapolis running game, as the Colts had 31 yards on the ground in the first half and 63 rushing yards through the first three quarters. As a group, their finest moment likely came at the start of the second quarter when Indianapolis had a first and goal at the New England one. On the first down play, Wilfork got great penetration and brought Joseph Addai down for no gain. After an incomplete pass, Ninkovich sacked Orlovsky for an eight-yard loss, forcing the Colts to settle for a field goal at the end of a 19-play drive. That defensive stand set the tone nicely for the first 45 or so minutes, at least until the Colts turned it on down the stretch.

By the numbers: Wilfork had 10 tackles (five solo). He also had a sack (for seven yards), as well as a quarterback hit and a tackle for loss. It was the most tackles he’s had this season, and he most since he finished with 10 in an overtime win over the Ravens last season.

Money quote: “It’s frustrating, but frustrating might be the wrong word; [it’s] more like a missed opportunity. It’s a 19-play drive. It’s a heck of a drive, so you don’t want to put a negative on that, but would we have scored a touchdown and do we need to? Yes.” -- Colts quarterback Dan Orlovsky (30-for-37, 353 yards, two touchdowns, one interception) on having to settle for a field goal at the end of their 19-play drive that stretched from the end of the first quarter to the start of the second quarter.

THE PATRIOTS AREN’T SHY ABOUT EXPERIMENTING WITH SOME NEW FACES

On both sides of the ball, the Patriots ran some new faces out there Sunday against the Colts. Some of it was because the Patriots were depleted by injury. Some of it was an attempt to get some people some reps at some different spots. And some of it was to make future opponents think about the possibility of some wrinkles going forward. On offense, Nick McDonald was pressed into service because of injuries to New England’s first three centers, and appeared to handle himself well. Meanwhile, the Patriots utilized lots of different faces on defense, including Niko Koutouvides at outside linebacker, Nate Jones and Matthew Slater at safety and Stevan Ridley at fullback. Of those out-of-position guys, Slater probably had the best afternoon, as the UCLA product (who started his career in New England as a safety) had seven tackles (six solo) and a forced fumble.

By the numbers: On Sunday, the Patriots started their fifth and six different safety (Nate Jones and Matthew Slater) and their ninth different outside linebacker (Koutouvides).

Money quote: “We are always saying that anytime you can do more, it helps the team. When you have guys that can play multiple positions, it gives them a profound understanding of the game overall and that will definitely help us.” -- Cornerback Antuwan Molden.