Smith’s long-term future with 49ers in question

And there we have it. The 49ers have placed QB Alex Smith on the injured-reserve list, meaning his season is over.

The bigger question is whether Smith will play again in San Francisco.

After this season, Smith will have two years remaining on the six-year, $49.5 million contract he signed in 2005, when he was the No. 1 overall pick.

Smith is scheduled to make $9.625 million next season, which is not happening. So the 49ers will have to approach Smith and ask him to restructure. But Smith must be willing to agree to a number and many around the league believe he will not be of the mind to do any favors for the 49ers. If the two sides cannot agree upon a lowered restructured number, then San Francisco will have no choice but to release him.

And if the 49ers cut him next year, they would have to count $5.332 million against their salary cap, although San Francisco always could designate him a post-June 1 cap-casualty and split the $5.332 million cap charge over two seasons. Their choice.

There were questions about whether Smith would return this season. Those will only increase next season, when Smith’s salary balloons to close to $10 million. Clearly Smith will not return to San Francisco under the current contract terms, if he returns at all.

At this point, it probably is best for both sides to move on — for Smith to get a fresh start elsewhere and the 49ers to go a different direction. But the direction they’ve gone now does not include Smith in any plans for this season.

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