Having suffered two ugly second-half collapses in the past two weeks, Jim Harbaugh‘s 49ers suddenly look like a team that lacks discipline and focus. Can they turn it around, and—more importantly—are they even Jim Harbaugh’s 49ers anymore?

Talking about “must-win” games before the halfway point in the season is often silly. Teams can get things turned around in a number of ways, and often do. But when it comes to the 49ers and their current predicament (1-2, having been outscored 38-3 in blowing halftime leads the past two weeks against the Bears and Cardinals), Sunday’s showdown with the Eagles sure feels like a must-win for San Francisco. This team needs to start to feel good about itself in a hurry, or the season could slip away.

That’s the feeling I got watching the 49ers’ 23-14 meltdown in the desert against the Cardinals. There were the three personal foul penalties against San Francisco in a little more than five minutes of game action. There were the three carries for 49ers running backs (one for Frank Gore) in the second half despite San Francisco’s 14-6 halftime lead.

There was the lack of pressure against Cardinals quarterback Drew Stanton (zero sacks, two hits, five hurries according to ProFootballFocus.com), which meant he could conduct business from the pocket like he was sitting in a La-Z-Boy. That further exposed a secondary that has been torched the past two weeks. You could understand it against the Bears, with Jay Cutler and his weapons, but Drew Stanton and rookie receiver John Brown?

And, finally, there was Colin Kaepernick, who continues to look like a franchise quarterback in the first three quarters of the game but just another guy when pressure mounts and he can’t use his feet.

San Francisco’s secondary was shredded by a rookie wideout, John Brown, 12, for two third-quarter TDs. (John Biever/Sports Illustrated/The MMQB)

Before I go any further, let me point out that the Cardinals are a very good team and a legit 3-0. The defense has not taken a big drop after the injury to Darnell Dockett, and defensive coordinator Todd Bowles did a tremendous job scheming for the 49ers. And it’s amazing what Arizona is doing on offense with less talent, especially with quarterback Carson Palmer out. The Cardinals are a well-coached team with Bruce Arians and will be a force in the NFC West for the rest of the season.

But these were (are?) not the 49ers we have been used to seeing since Jim Harbaugh took over in 2011. You could count on San Francisco to be a well-coached, disciplined defense-first team that relied on a power running game with a few athletic plays from Kaepernick sprinkled in.

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In the past two weeks we’ve seen an undisciplined team that easily loses its cool and can’t recover when things go bad. That’s an indication, in my opinion, that the Niners players are no longer drawing their persona from the head coach, and are instead doing things their own way. That’s a bad sign.

When Harbaugh spoke with Anquan Boldin on the bench after his personal foul penalty, the coach appeared dumbfounded and speechless. Later in the fourth quarter, when the broadcast showed Harbaugh on the sideline, he looked as if he had no answers for a team that desperately needed him to lead them out of that malaise.

Is Harbaugh getting through to his players anymore? And will he be around much longer? (John Biever/SI/The MMQB)

The players’ disposition and the coach’s increasing disconnect with his team look familiar to me: The situation reminds me of Nick Saban as he coached the Dolphins during their 1-6 start to the 2006 season, when they were a preseason Super Bowl favorite. It wasn’t long before Saban started looking at other options, which led to him taking the Alabama job. The players knew he wasn’t all in, and it all ultimately collapsed.

Harbaugh is in the fourth year of his five-year contract, and both sides have tabled contract talks. With Harbaugh’s alma mater, Michigan, just 2-2 this season with blowout losses to Notre Dame and Utah, there is only going to be increased chatter of Harbaugh’s future.

The offense, with Harbaugh increasingly calling the plays, has become more and more reliant on Kaepernick. Yes, the 49ers were without their top two tight ends (Vernon Davis and Vance McDonald), but there are still creative ways to run the football.

If we’ve learned anything about Kaepnerick to this point in his career, it’s that he’s not capable of carrying the 49ers against the better defenses in this league. Yes, he was 29 of 37 for 245 yards (103.3 rating), but stats lie. The truth is that if the 49ers don’t have the threat of the play-action pass, Kaepernick can’t get a defined read. If he doesn’t have that, he becomes indecisive and fails to see open receivers. Kaepernick has a difficult time feeling and dealing with pressure in the pocket. If he senses pressure (and sometimes it wasn’t even there against the Cardinals), his flight sense kicks in. He needs more fight, which in quarterback terms means to move within the pocket with eyes downfield and make a play from the pocket.

No matter how athletic the quarterback is, NFL games still come down to making plays from the pocket. This is why Russell Wilson continues to ascend, while Kaepernick is the same player he’s been, if not regressing. Wilson flourishes when the game and pass coverage is the tightest, late on. Kaepernick gets worse.

The 49ers haven’t scored a fourth-quarter touchdown since Kaepernick hit Davis with 10:31 left against the Packers in last year’s wild-card game. That’s five-plus games without a fourth-quarter score. The best teams and players rise to the occasion later in the game. The 49ers and Kaepernick continue to come up short.

The 49ers’ defense, hurting without NaVorro Bowman and, especially, Aldon Smith, hasn’t been up to its usual standards, but has played well enough to win the past two games. It’s Harbaugh, Kaepnerick and the offense that have failed to deliver. If they don’t do it Sunday against the Eagles, it may be too late.