The notion that the 49ers have gone beyond expressing interest in free agent Peyton Manning but actually watched him work out likely energizes the fan base a lot more than the players on the roster.

Of all those players, none should be more perplexed than Alex Smith, San Francisco’s own free-agent quarterback.

Smith, you might recall, is the guy coach Jim Harbaugh persuaded to return for the 2011 season. Alex responded by with his best season, leading the 49ers to the NFC Championship game.

Smith and Harbaugh seem to have built the kind of relationship all quarterbacks wish to have with their head coach. There were mutual expressions of admiration, mutual shows of support and consistent statements between the two.

Did anybody buy into Harbaugh’s blue-collar mentality more than Smith? He often, and proudly, wore his blue work shirt with the “Alex” label affixed to the front.

Meanwhile, Harbaugh consistently — and emphatically — insisted Smith is his quarterback.

Moreover, the rest of the offensive unit took its cues from Harbaugh, lining up in lock-step to support Smith, whose first six seasons had offered a vast array of disappointment, from poor performance to several injuries to constant turnover among offensive coordinators, resulting in a different playbook and system each season.

In the months since the NFC Championship game, every signal sent by Harbaugh and Smith has indicated they will remain intact, implying Harbaugh’s unwavering loyalty was sincere. Smith surely presumed he would re-sign, anticipating a multiyear contract.

Suddenly, five days after signing controversial free-agent wideout Randy Moss, the Niners are chasing Manning, the future Hall of Famer trying to resurrect his career despite multiple neck surgeries as he approaches his 36th birthday.

It’s quite the intriguing possibility, the visual of Manning throwing to Moss.

It also reeks of risk. Is Moss truly committed? Can Manning stay healthy? Do Harbaugh and general manager Trent Baalke really want to dramatically alter a team that in 2011 exceeded anyone’s wildest expectations?

Most important, though, does Harbaugh want to put his integrity on the line?

That’s what he’d do if Manning signs with San Francisco. The implicit message to everyone in the locker room: Watch what I do, not what I say.

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