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SANTA CLARA — When you’re watching the 49ers play the Falcons this Sunday in Atlanta, and the Niners take an early lead, and their offense looks terrific, and the Falcons look confused, and you say, “Gee, the Niners might win!” and then they blow their lead, and their offense looks terrible all of a sudden, and they end up losing by two touchdowns, you probably will ask yourself the following question:

Why does Chip Kelly’s offense work only in the first half?

Kelly amazingly let the answer slip this week at his Monday press conference. All season, he avoided this question. Throughout his franchise-record 12-game losing streak, reporters have asked him to explain why his offense looks potent in the first half and so utterly inept in the second. What is the pattern, Chip? Why does your offense gain an above-average 5.7 yards per play in the first half and a putrid 4.3 yards per play in the second? Can you give us any insight?

Until Monday, Kelly has offered zero insight. He simply repeated plays as if he was reading straight from the game book. On second-and-6, the right tackle committed a holding penalty. On third-and-16, the tight end dropped a pass. And so on and so on. As if there is no pattern. As if the second-half offense has been a victim of a series of unfortunate events. Right.

It’s obvious why Kelly filibusters: If he answers truthfully about his second-half offense, he would expose the reason the 49ers should fire him, and he doesn’t want to give anyone that ammunition. But on Monday, he did. By mistake.

A reporter reminded Kelly that Carlos Hyde had “a really good game” against the New York Jets the day before. Which was true. Hyde rushed for 193 yards and also caught a touchdown pass. He was the 49ers’ entire offense.

But for some reason, Hyde played only a little more than half the game. Was on the field for just 30 of the Niners’ 57 offensive snaps. His backup, Shaun Draughn, was on the field instead of Hyde for 27 snaps.

“Was there a conditioning aspect of it with Carlos?” the reporter asked Kelly. “Was Hyde winded?”

“Yeah,” Kelly admitted. “There were a couple times after the long runs when he took himself out. But, you understand because of the long runs. (Running backs coach Tom Rathman) wasn’t trying to get an even-steven deal. He was just trying to keep (Hyde) fresh.”

Bingo. Kelly finally incriminated himself, and didn’t even realize he had.

According to Kelly, Hyde took himself out of the game after long runs because he was too tired to sprint back to the line of scrimmage for the next play. This was entirely Kelly’s fault. Remember, the Niners don’t huddle. Kelly’s scheme is “up-tempo” — it’s the fastest offense in the NFL. Players run a play, then run back to the line of scrimmage, then run another play, then run back to the line of scrimmage over and over and over. Run run run run run.

Almost every time Hyde took himself out, the coaching staff kept him on the sideline for long stretches so he’d be “fresh” when he went back in. “Fresh” being the key word.

When Kelly’s players are fresh — i.e. during the first quarter — his offense works. We see this every week.

Take last week against the Jets. The Niners led 14-0 after just four minutes and 15 seconds, then scored three freaking points the rest of the afternoon.

The Niners’ first touchdown came as a result of Jets quarterback Bryce Petty throwing an interception at his own 7. The Niners scored a touchdown the very next play. This was the Niners’ first possession of the game.

The second touchdown came as a result of the Niners’ one and only long drive. This was their second possession, and it lasted just 1:49.

The first play was an 11-yard run by Hyde. After he got tackled, all 11 players on the Niners’ offense jogged to the line of scrimmage and quickly ran the second play – a 19-yard completion to Quinton Patton. After he got tackled, all 11 players on the Niners’ offense jogged to the line of scrimmage and quickly ran the third play – a 47-yard run by Hyde. He got tackled from behind at the Jets’ 4.

Hyde was gassed, so he took himself out and Draughn replaced him and scored a touchdown on a run up the middle. Four plays, 81 yards, and only one substitution which came at the end of the drive. Kelly’s up-tempo offense kept the Jets on their heels.

Kelly’s edge is the pace of his offense. When he can string together play after play after play without interruption, his scheme is tough to stop.

But, he can’t string plays together all game because his players get tired. And they take themselves out, which allows the other team to make substitutions. The opposing defense subs players only when the offense does.

In the NFL when the offense makes a substitution, an official stands over the ball and prevents the offense from running another play until the defense makes its substitutions, too.

Against Kelly, opposing defenses take as much as time as possible to sub players. They waste Kelly’s time. Make his guys stand and wait as the other team shuffles players on and off the field and the play clock ticks. And when the defense is finished and the official standing over the ball finally moves, the offense sometimes has just 10 seconds to line up and snap the ball.

And that means the opposing defense takes away Kelly’s edge — his tempo. All Kelly has left after those substitutions is his simple playbook — it’s by far the simplest in the NFL — against the other team’s sophisticated playbook. And he gets crushed.

After that one glorious hyper-speed touchdown drive against the Jets, Kelly had to substitute his fatigued offensive players 27 times. Twenty-seven.

In a world where football players don’t get tired, Kelly would be the best coach. But they do get tired, and that’s why Kelly’s scheme doesn’t work in the NFL. And that’s why he will get fired.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for The Press Democrat’s website. You can reach him at grantcohn@gmail.com.