49ers Notes: Offseason surgeries, Aiyuk’s contract, Wilks’ future, and OT rules

Tuesday was a deeply brutal morning for the San Francisco 49ers. The Super Bowl hangover is a ruthless one, especially as reporters invade the locker room following a crushing loss.

Both Kyle Shanahan and John Lynch addressed the media, along with the majority of key players. Here’s what came out of it.

Surgeries coming
Arik Armstead revealed Tuesday that he decided to play through a torn meniscus in the second half of the season, and that he would require offseason surgery. Clelin Ferrell also sustained a torn meniscus that ended his season.

So, too, will Dre Greenlaw, who suffered a torn Achilles entering the game from the sideline. Fred Warner said he knew fairly quickly what the injury was because of Greenlaw’s reaction and the fact that he had been playing through an Achilles injury.

“I knew what it was right away just because of the way it happened and his pain on the ground. I knew he was dealing with an Achilles for a while now, so it wasn't a shock to me.”

John Lynch volunteered that Armstead wasn’t the only one playing hurt. He said that Javon Hargrave has been playing through a torn thumb ligament.

Aiyuk’s contract and other offseason priorities
It’s not the offseason without a receiver taking cryptically to social media before he’s due for a major contract extension.

See:

On Instagram, Aiyuk posted a story that said “Don’t forget what you got there 👀,” while his friend, Draysean Hudson posted a story reading:

“This is the exact reason why we leaving San Francisco
Thank you 49ers for drafting my brother we are forever grateful
BA to Vegas 🏴‍☠️”

Rochelle Searight, Aiyuk’s girlfriend, and mother of his son, Braylon, said “This might’ve been the last day we touched foot on Levi’s Stadium, me and Braylon, because we might not be out here next season.”

Now, Aiyuk is an elite wide receiver who is massively underappreciated, and was open on key downs in which he could have won the Super Bowl for the 49ers. He was targeted six times for three catches for 49 yards and a touchdown, while Deebo Samuel, who had zero ability to separate from Chiefs corner Trent McDuffie, was targeted 11 times for three receptions, for 33 yards.

I asked Brock Purdy about the 3rd-and-5 with two minutes left, when Aiyuk’s defender, Trent McDuffie, blitzed off the edge. The 49ers weren’t ready for it, and while Purdy threw hot to Jauan Jennings, he admitted Tuesday that the ball should have gone to Aiyuk, who was wide open with a safety covering him.

Aiyuk didn’t do all that much to calm the speculation. Asked if he wants to stay in San Francisco, he was noncommittal.

“If that’s the right move, yeah.”

What would make it the right move?

“Being a champion,” Aiyuk said.

The newly-minted All-Pro and Pro Bowl receiver got emotional when he was asked about what this season meant to him.

Lynch was asked about Aiyuk’s contract status, and didn’t get too specific, but said the 49ers obviously want to retain him.

“You have to prioritize all these things,” Lynch said. “Brandon's entering his fifth-year option. Brandon's been a fantastic player for us. Kyle calls him a warrior all the time because of the way he goes out and competes that shines through. Whether you're a trained eye or whether you're a fan, you can see the passion he plays with, you can see the production that he's had. We're extremely proud of what he's become. And he should be as well.

“And so your team is comprised of guys, veterans, who've been paid very well, of guys who want to be paid very well. We've got one guy on our team (Brock Purdy), who is pretty prominent, who can't be paid very well right now because the CBA doesn't allow, so it's all one big puzzle.

“We've developed a good cadence over the years, Kyle and I, where he focuses on the season, we do all the planning, and then we present things to him and we work through it, and that's what we'll continue to do. But of course, you want a guy like Brandon Aiyuk to be a part of you going forward.”

The 49ers are known for both paying their top players heading into their fifth-year option, but simultaneously notorious for leading negotiations in a way that is protracted and laborious for both sides, frequently leading into training camp. Nick Bosa said Tuesday that his holdout affected his play negatively from a mental and physical standpoint.

Aiyuk proved that he is an elite wide receiver this season. Wide receivers coach Leonard Hankerson told me on Monday of Super Bowl week that Aiyuk is the NFL’s WR1, and that his growth as a receiver from a mental standpoint has been “elite.”

“I don’t think he’s ‘probably’ the best receiver in the league,” Hankerson said. “He is the best receiver in the league… I’m not sure why he’s under the radar.”

Hankerson proceeded to say exactly why Aiyuk’s under the radar, articulating part of the reason he might have some frustrations. He is the most efficient, elite receiver in the league, but he doesn’t get targeted the same way some star receivers do.

“He’s gone from 700 yards to 800 to 1,100 to now 1,400, almost 1,500 yards, what more can you ask for?” Hankerson said. “To go out there and be on a team where he can catch 100 balls? That shouldn’t matter. He’s putting up numbers on a team where we’re not throwing a ball 50 and 60 times a game.”

Those frustrations tend to loom a little larger when the difference between winning and losing a Super Bowl is not targeting Aiyuk, and the fact that he’s probably hearing other teams are willing to pay him, while negotiations with San Francisco (while on $14.15 million fifth-year option), will be difficult. Still, the odds the 49ers trade him are slim. It would be incredibly foolish to trade the best receiving option on their offense.

Steve Wilks’ future not confirmed
If you wanted Kyle Shanahan to give his seal of approval, a vote of confidence, or whatever you want to call it, on Steve Wilks… you’re going to leave empty-handed.

Shanahan was asked twice about Wilks’ future and whether he expected him to remain with the 49ers. While he said he expected all the 49ers’ coaches to stick around, he didn’t guarantee Wilks explicitly. That comment also ignores the reports that passing game coordinator Klint Kubiak has reached a deal with the New Orleans Saints to become their offensive coordinator.

Here’s what Shanahan said on Wilks. First he was asked about Wilks and the defense’s performance. He latched onto the defense.

“I thought they were one of the reasons that we got this far,” Shanahan said. “I thought they did a number of good things, thought they did a lot of good things in that game too. Just like our whole team. We did a bunch of good things this year, but came up short in the last game.”

This follow-up was asked about Wilks:

“Kyle, on Steve Wilks, have you guys spoken on this stage in his career, and where you want the team to go, is there any reason to think he won't be back next season?”

Shanahan’s response was a bit vague, and it was unclear whether he was talking about conversations with Wilks, or, more likely, Lynch.

“No, that's something - we'll talk about a ton as this week goes, we'll talk about a ton in the offseason, I mean where we want our team to be, our defense, our offense, special teams and that's a lot of conversations, a lot of film, a lot of personnel and salary cap we got to discuss, draft,” Shanahan said. “I haven't even watched the game yet to tell you the truth.”

Given the lack of clarity, a direct follow-up was asked later on whether Wilks is returning.

“I haven't talked to anybody yet,” Shanahan said, after hesitating at the start of his answer. “So yeah, I expect all our coaches to be back.”

So, technically it was a yes, Wilks will be back. But there was a very direct way for Shanahan to confirm that, and he didn’t take that route.

No meeting held on OT rules
Much was made of the fact that the 49ers opted to receive the kickoff in overtime. The logic, as Shanahan stated, was that if it came down to a third possession, the next score would win. The problem with that logic is twofold. First, the team that receives does not know what the outcome of the next possession will be.

The second team gets the benefit of that knowledge to choose how they want to approach the game. For the first team, it’s essentially four-down territory until you reach field goal range. For the second team, if you’re trailing by a touchdown, you know you have four downs all the way down the field.

Oh, and if the second team scores? They’re likely going for two, with the knowledge that the other team will get the ball back with a chance to end it. Patrick Mahomes said that was the Chiefs’ plan.

He, and other Chiefs also said that Andy Reid had his players prepped on the overtime rules with meetings on them each week of the season (though Mecole Hardman was unaware).

The 49ers did not. Kyle Juszczyk said after the game he was not aware of what the rules were.

Shanahan said Tuesday that he held no such meeting with his team during the week. He said that right before the overtime coin flip, he told his position coaches to go over the rules with their players, though many were still unaware. Brock Purdy confirmed as much, saying he confirmed the rules at that time with quarterbacks coach Brian Griese.

The head coach said the decision on the coin flip was based on discussions with analytics staffers, and that while he will sometimes disagree with them, the fact that neither offense was thriving was a factor.

Lynch also tried to come to Shanahan’s defense by pointing out that the 49ers’ defense had been gassed at the end of regulation.

“Some other context, I believe we just closed, I think it was an 11-play drive that we just closed the game with,” Lynch said. “And when you're playing Mahomes, you're chasing him a lot. So there's a lot of effort that's expended. I think the context from there is that you need some time to get fresh. And so all those things play into it and those were sound decisions.”