Naturally, everyone wonders why teams don’t just run their hurry-up offense all the time.

”It’s a totally different situation there at the end. I’ve been asked that a lot,” said quarterback Alex Smith, who led the Chiefs through a near-flawless two-minute exercise in their victory at Denver on Sunday night. ”You want to play like that all the time but it’s different.”

Smith had a hard time explaining why it’s different, but that doesn’t change the reality. The Chiefs struggled simply to pick up first downs until they were faced with an eight-point deficit in the closing minutes, and marched 42 yards for the tying touchdown and 2-point conversion. They went on to win 30-27 on a field goal by Cairo Santos in overtime.

”That defense is a good defense and they have game-changing players,” Smith said. ”You look back at their Super Bowl run, the sack-fumbles, the touchdowns and the things they can create. I know we didn’t have success early, but we didn’t give them those. We eliminated those. Those are the things teams feast off of. We were able to hang around and make adjustments. And then we were able to make plays down the stretch.”

The Chiefs have been criticized all season for their offensive production, which ranks in the bottom third of the NFL in most major categories. Smith has endured the brunt of it, too, not only as the most visible part of the offense but also because of his own erratic play.

He’s missed open wide receivers. He rarely pushes the ball downfield. He has been reluctant to run. And he seems content to check down at the first sign of trouble.

But when the pressure was Sunday, the veteran quarterback responded. He kept finding unheralded wide receivers and tight end Travis Kelce for first downs, and he threw a dart to Tyreek Hill with 12 seconds remaining in regulation to help force the extra session.

”Yeah, it’s weird, but I think the crazier it gets, the calmer he is,” Chiefs coach Andy Reid said this week. ”That’s just how he’s wired. It seems to just calm everybody else down. It’s a unique thing. It’s one of the things that makes him a great player, I think. He handles that very well.”

It wasn’t always this way. The Chiefs have struggled going into halftime and at the end of games the past couple of years. But they spent extra time on the two-minute drill during the summer, and again in training camp, and it has paid off in a big way this season. They needed a similarly frantic comeback to beat San Diego in their opener.

So again, shouldn’t the Chiefs want to run that tempo all the time?

”The obvious answer to that is yes,” co-offensive coordinator Matt Nagy said, ”but you don’t get away from what your identity is as an offense. And you have to understand, the defense is playing differently when you’re in the two-minute mode, too.”

The Chiefs (8-3) head to Atlanta on Sunday before turning around to face Oakland on a short week at Arrowhead Stadium. Both offenses are dynamic, and the Falcons’ may be the best in the NFL, so there will be pressure on Smith and the rest of the Chiefs offense to keep pace.

At least, for the first three quarters.

They seem to do just fine in the final minutes of the fourth.

”A lot of games in this league come down to that,” Smith said, ”so it’s something we work hard on. It’s one of those things where the more you practice it, the better you are at it. It’s all of us being better in a situation like that.”

Notes: DL Kendall Reyes (knee) and DT Dontari Poe (back spasms) did not work Thursday. … Santos was chosen the AFC special teams player of the month. He went 11 for 11 on field goals in November, including that overtime winner against the Broncos.

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The Chiefs planned to add the four-time Pro Bowl linebacker to their roster after practice Wednesday, which was the deadline to make the move or put him on injured reserve. And while it’s far from certain that Houston will play against the Panthers, this is the first time all season it has been a remote possibility.

“You’re talking about one of the elite players in the league, especially when it comes to getting after the quarterback,” said Smith, who missed last week’s game against Jacksonville with a head injury, “and then his presence and his leadership is something everyone feeds off.”

It was a day of mixed injury news for the Chiefs.

Along with Smith returning to the first-team practice, running back Spencer Ware was cleared through the league’s concussion protocol and could play against Carolina. But not joining them on the field was wide receiver Jeremy Maclin, who hurt his groin in their 19-14 victory over the Jaguars.

As for Houston, he’s been working out for several weeks, slowly ramping up the load after having surgery in February on a bothersome ACL in his left knee. The injury happened midway through last season and the Chiefs shut him down, thinking at the time it was merely a hyperextension. But he struggled in two playoff games and ultimately required a procedure to repair the ligament.

While the Chiefs (6-2) have ripped off four straight wins, taking off some of the pressure of getting him back on the field, there is no question their pass rush could use his prowess.

They only have 16 sacks, putting them in the bottom third of the league, and nine of those belong to Dee Ford, who will no doubt find it harder to get the same kind of pressure without some help.

Chiefs coach Andy Reid said Wednesday he’s not sure what his lineup will look like once Houston is back. He praised the jobs Tamba Hali and Frank Zombo have done this season, but the reality is neither of them has offered much of a pass rush.

Still, that doesn’t mean Reid will rush Houston back onto the field.

“We just want to make sure he’s safe going out there and playing,” Reid said late last week. “I’m not sure we probably realize how severe of an injury he has there. This guy has really pushed through. His work ethic has just driven him to this point, right here. He’s been a beast on this thing, so it’s been fun to watch, but tough to push through. He’s done great with it, though.”

Meanwhile, Ware’s return couldn’t come soon enough.

Fill-ins Charcandrick West and Knile Davis were largely stuffed by the Jaguars last Sunday, and now Kansas City is preparing to face one of the best defensive fronts in the NFL. The Panthers are allowing 77.5 yards rushing per game, third best in the league, and Star Lotulelei, Kawann Short and the rest of them are tops in the NFL when it comes to yards per carry.

Smith should also help in that respect. He is more elusive than backup Nick Foles, who did just enough to help Kansas City beat the Jaguars, though Smith is running less this season than in past years.

Smith said missing one week shouldn’t slow him down, either. He ran the scout team most of last week, so he was still getting work in, and warmed up on game day as if he was the starter.

“It’s nice to have done that last weekend,” he said, “be able to kind of move forward like normal.”

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Kansas City will trade its second-round pick in the 2013 draft — the second selection (No. 34 overall) in the round — as well as another conditional mid-round pick in 2014 to acquire Smith from San Francisco, a league source told ESPN.

The 49ers now own 11 picks in the 2013 draft.

As a result of the trade, the Chiefs are expected to release former starting quarterback Matt Cassel, league sources told ESPN. Cassel has two years remaining on a $63 million, six-year deal he signed with Kansas City after he was acquired in a trade from the Patriots in 2009. He failed to live up to the lofty contract, however, and was benched during the 2012 season.

At this point, Smith will play under the terms of his remaining contract, which calls for a guaranteed base salary of $8.5 million in 2013. There have been no discussions between the Chiefs and Smith’s representatives about negotiating a new contract.

49ers left tackle Joe Staley, one of Smith’s closest friends on the team, said in a text to ESPN NFL Insider Ed Werder that he was happy the quarterback will get a chance to play with his trade to Kansas City.

“I am happy he is going to get a shot to play somewhere. He is too talented not to. Will miss him on our squad but will still be close wherever he goes. Happy for his new opportunity,” he wrote in the text.

9ers tight end Vernon Davis, who developed a great on-field chemistry with Smith in the team’s passing game, also wished the quarterback the best with his new team in another text to Werder.

He wrote: “I will miss him dearly and wish him the best as he starts something new. I’m sure everything will work in his favor. He is definitely a great player who I strongly believe had a big impact on my career. Love you Alex!”

The trade can’t be officially completed until March 12 when the 2013 league year begins.

The trade agreement was first reported by Fox Sports.

Smith, the 2005 No. 1 overall draft pick, lost his starting job to Colin Kaepernick while sitting out with a concussion but was professional at every turn and continued to mentor his replacement.

Before his injury, Smith had completed 26 of his last 28 passes — including going 18-of-19 for 232 yards, three touchdowns and no interceptions in a “Monday Night Football” win at Arizona on Oct. 29.

He then sustained a concussion in the second quarter of the 49ers’ next game, a 24-24 tie against St. Louis on Nov. 11. Smith sat out the next game as Kaepernick dazzled in his debut as an NFL starter, beating the Bears handily at home on “Monday Night Football.” Smith didn’t start again last season.

The 28-year-old quarterback has thrown for 14,280 yards with 81 touchdowns and 63 interceptions in 80 career games.

The Chiefs hired Andy Reid as their new coach this offseason after a 2-14 season that led to the dismissals of coach Romeo Crennel and general manager Scott Pioli but earned Kansas City the No. 1 overall pick.

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Browns offensive coordinator Norv Turner worked well with Smith in San Francisco when he was the team’s offensive coordinator in 2006 and Chiefs coach Andy Reid has expressed an interest in Smith in the past, making Cleveland and Kansas City two possible destinations.

There’s one other factor to consider: If San Francisco deals Smith instead of cutting him, it would save the $1 million or $2 million roster bonus it would have to pay if he is released.

Smith, the 2005 No. 1 overall draft pick, lost his starting job to Colin Kaepernick while sitting out with a concussion but has been professional at every turn and has continued to mentor his replacement.

In fact, coach Jim Harbaugh has indicated that Smith spends more time than he does coaching Kaepernick.

Before his injury, Smith had completed 26 of his last 28 passes — including going 18-of-19 for 232 yards, three touchdowns and no interceptions (good to a 157.1 passer rating) in a “Monday Night Football” win at Arizona on Oct. 29.

He then sustained a concussion in the second quarter of the 49ers’ next game, a 24-24 tie against St. Louis on Nov. 11. Smith sat out the next game as Kaepernick dazzled in his debut as an NFL starter, beating the Bears handily at home on “Monday Night Football.” Smith didn’t start again this season.

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