SANTA CLARA, Calif. — The San Francisco 49ers threw down the gauntlet to Brandon Aiyuk on Wednesday in the most dramatic moment of a tense game. Then the clock ticked and expectations soared.

Will Ayuk come to training or not?

“We’ll see what happens. I think you’ll see that with me. I know he’s here today. That’s what’s expected,” general manager John Lynch said at a news conference about 20 minutes before practice began.

So camera crews and reporters headed to the stadium to see if Aiyuk would show up for his first practice with the 49ers since the Saturday before the Super Bowl in February. Earlier, head coach Kyle Shanahan and Lynch had made it clear they were no longer tolerating Aiyuk’s claims that he wasn’t healthy enough to practice, even announcing that team doctors had cleared him to do so. His “abstention” — attending meetings to avoid fines but not practicing to protest the lack of a new contract agreement — was over in the 49ers’ eyes. He had to practice or face the consequences.

At the start of the session, the players stretched and jogged, then went to practice. Everyone was watching. Aiyuk was not present and was not registered. No contract agreement had been reached. In any case, Aiyuk did not give in to the increasing pressure from the 49ers to start practice.

Quite frankly, the signs seemed to point more to an imminent breakup than any imminent breakthrough.

“At some point, you have to play,” Lynch said before leaving the show, summing up the frustrations of the moment.

But he also added: “I’ve seen these things look bleak before and they can change quickly. This gives you hope. We’ve been through these situations before and these things can be forgotten quickly.”

But there was no doubt that the San Francisco 49ers’ leaders had identified Wednesday as a turning point. And it made sense. I’ve been critical of the way the 49ers handled the Aiyuk situation, but this moment was inevitable. The 49ers couldn’t afford to keep an inactive Aiyuk on the active roster as they raced toward the regular-season opener on Sept. 9 against the New York Jets. They certainly wouldn’t pay him his Week 1 paycheck if he made himself unavailable. To put themselves in a position to cut him, they had to start taking drastic measures.

Will Aiyuk be penalized for missing practice? “I’ll deal with it when it happens, if it happens,” Shanahan said before the hearing.

Shanahan was clearly in a bad mood while talking about Aiyuk on Wednesday, and that mood couldn’t have been bettered once he saw that Aiyuk was missing practice. Under CBA rules, the 49ers can fine Aiyuk $6,403 for the first time for missing practice, a meeting or curfew, then $11,206 for the second and $16,009 for the third. The maximum daily fine is $45,769. After multiple fines, the 49ers can suspend Aiyuk.

I believe the 49ers have already fined Aiyuk for his foul on Wednesday. He could be suspended in a few days. I’m not saying bridges will be burned all at once, and if they do, we might be able to smell the smoke.

But the bottom line is that the 49ers want Aiyuk to practice and need him to play. Without him, their offense and their team would be worse off. They challenged him by making trades to several teams, but Aiyuk rejected those options and the 49ers resumed contract negotiations. They made several contract offers. I think the 49ers could have been more aggressive with their financial offers in the face of a wide receiver market that has exploded this year or they could have realized how bad things are and traded him in April. If they end up divorced, they will regret it.

But even just a few days ago, a deal seemed possible. It was almost expected. But nothing happened. And on Wednesday, the moment of defiance and rejection came.

Somehow, whether by chance or not, the 49ers have pushed Aiyuk into becoming an official opt-out along with standout linebacker Trent Williams, who is also away from the team’s headquarters seeking a new deal. That might actually cool things down a bit, at least temporarily. If he opts out, Aiyuk can move to the reserve list (along with Williams as well) and not count against the roster cap. The 49ers don’t have to hold him to avoid paying the playoff check, because he wouldn’t be eligible for it.

The 49ers won’t have to see Aiyuk the way they have throughout camp. They won’t have to wonder if they’ll be photographed standing next to him or shaking his hand during practice. Out of sight, out of their personal space. That’s one of the ways Williams’ situation has been calmer, and why Shanahan and Lynch remain optimistic that Williams will return to camp within the next few days.

But the 49ers still have to come to an agreement with Aiyuk or try to force him to play out his $14.1 million contract this season. If a deal isn’t reached soon, it’s probably safe to assume Aiyuk will at least skip the first few games and possibly reach the age of six in time to qualify for free agency next offseason. The 49ers could still retain his rights by putting the franchise tag on him for 2025, but by that point, would it be worth continuing the relationship?

It’s a bitter road, but perhaps the most likely at this point. An even more bitter question for 49ers fans: Assuming the difference between the 49ers and Aiyuk isn’t much more than $10 million guaranteed, are the 49ers being short-sighted and cheap right now? Obviously, Jed York has committed a huge amount of money to this roster, but that’s what happens when you’re trying to win a Super Bowl. Are the 49ers unwilling to commit what it takes to give themselves the best chance? Are they more interested in winning contract negotiations than winning the playoffs?

“First of all, I don’t think you can ever assume you’re ready to play in the Super Bowl,” Lynch said. “You have to win it every year. Nothing is guaranteed in this championship. And we have a very talented team, we have a proven team that has won a lot of games. But this is a new team. We love our team. We feel like we’ve improved.”

“Yes, this team has never lacked resources. Since we’ve been here, we’ve been one of the highest-spending teams in the league. And I think there’s a reason for that. We have a lot of good players. We’ve been successful in attracting talent, both through the draft and through trade. And as a result, we’ve had a lot of great players … at their positions. That’s good. But it makes things more difficult. That’s our challenge.”

The 49ers are facing a lot of challenges right now, just when they should be feeling pretty good about the season. Instead, they’re facing a contractual meltdown that could leave them a less talented team. Or maybe two. It’s the biggest managerial challenge the team has faced in a while. And on Wednesday, they addressed it by issuing their own challenge to Brandon Aiyuk, who hasn’t backed down for now.

It was very dramatic. It was inevitable. It was understandable. But like almost everything else over the past few months with this issue, they got nowhere.

(Photo by Brandon Aiyuk: Lachlan Cunningham/Getty Images)