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There seemed to be optimism for Deebo Samuel’s return by Week 1 after a Jones fracture this offseason. Samuel took to Twitter on June 18 to say he’d be back after 10 weeks, which would have been around August 27. That is clearly not the case.

Per the 49ers, Samuel will be placed on injured reserve. Unlike in previous years, the wait time to return from injured reserve is just three games from the previous six weeks, and an unlimited number of players can be placed on injured reserve and later return. That limit was previously set at three players. According to NFL Network’s Ian Rapoport, the team is hopeful Samuel can return in Week 4.

Transactions: The #Patriots promote K Nick Folk to the 53-man roster; The Jets signed QB Mike White to their active roster; The #49ers placed WR Deebo Samuel on IR, and they’re hopeful he’ll play in Week 4; The #Bears activated K Cairo Santos.

— Ian Rapoport (@RapSheet) September 12, 2020

Once he returns to practice, he’ll have a three-week window to either be promoted to the active roster or return to injured reserve for the remainder of the season.

Head coach Kyle Shanahan explained Friday why the team declined to place him on injured reserve from the outset, saying he’d be “day-to-day.”

“Because we believed he had a good chance to play this week,” Shanahan said. “It didn’t go the way we hoped, but he’ll still be day-to-day going on that next week. We felt there was a chance, so to make a decision that would be three weeks when we thought he did have a chance. We didn’t think that would be very smart, but we’ll see how next week goes. Also, it’s something with the rules that because it happened before training camp started, which is considered non-football injury, there was some reason we couldn’t do that, either.”

What Shanahan was referring to is the fact that Samuel’s injury was a non-football injury (NFI).

If the 49ers elected to keep him on that NFI/reserve list rather than place him on the active roster, they’d have to keep him out for a minimum of six weeks, rather than the three games required under the injured reserve list. It’s basically identical to the physically unable to perform (PUP) list rules.

In essence, this could have been the team’s plan the whole time, but keeping him on the active roster gave them an opportunity to evaluate his health, give him a chance to play in Week 1, and if not, shelve him for half the time that would have been required under NFI rules.

We explained here why Samuel’s injury, the same one which Trent Taylor lost his 2019 season to, is so complicated.

The main issue is that the outside part of the foot gets terrible blood flow, just about as poor as anywhere else in the body, which inhibits healing. Typically, though, NFL players return from Jones fractures in 8-10 weeks. Samuel, clearly, will surpass that by some margin, as he has already crossed the 12-week threshold. A return in Week 4 would place him at the 15-week mark. It’s unclear if this is the result of complications, slow healing, or an abundance of precaution on the 49ers’ part.

Additionally, the team promoted center Hroniss Grasu and cornerback Dontae Johnson from the practice squad. New practice squad rules allow much more flexibility in practice squad machinations. Aside from the increased number of players (from 10 players in prior years to 16 this season), players can be promoted to the gameday roster twice and then returned to the practice squad. This means the 49ers will retain Grasu and Johnson on the practice squad after this week and can promote them each one more time while still retaining them there.

They, along with wide receiver Kevin White and defensive end Dion Jordan, were among the four players the 49ers elected to protect this week. That’s another new rule this year, allowing teams to prevent four practice squad players each week from being poached by other teams.

Grasu provides cover for Ben Garland (new NFL rules also allow for an extra reserve offensive linemen to be added to the active gameday roster this year and be activated in-game if an offensive line injury occurs). He could start if Garland sits, or back up Daniel Brunskill, who could also start at center if Garland is out. Brunskill would likely start at right guard if Garland is active.

Dontae Johnson gives the 49ers an extra corner with Jason Verrett out with a hamstring injury. It’s also significant given that the Arizona Cardinals use three wide receiver sets more than any team in the NFL. If the 49ers were, say, to use dime (two safeties, four corners) or big nickel packages (three safeties, three corners), an extra corner would be a necessity.