That quarterback might be Washington Redskins signal-caller Kirk Cousins. Washington has until July 17th to sign its quarterback, whom it franchise tagged for the second-straight year, to a long-term deal. Failing to do so would likely make him a free agent in 2018 and free to sign with the 49ers or any other NFL franchise.
Shanahan was Cousins' offensive coordinator in Washington from 2012 until 2013 and the two share mutual respect for one another. Should Shanahan and Cousins not be able to reunite in San Francisco, the team could pursue a quarterback in the 2018 NFL Draft, as the class of signal-callers is seen as being much stronger than this year's incoming crop of rookies.
Of course, a lot could happen before then. One of the quarterbacks on the 49ers' roster could emerge as a possible long-term solution. That could be Hoyer or his 2016 Chicago teammate, Matt Barkley. The 49ers also used a third-round draft pick to select C.J. Beathard out of Iowa in April. Beathard was reportedly the only quarterback on the team's draft board and the only one whom head coach Kyle Shanahan saw as a fit for his offense and possessed the quarterback traits that he covets.
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At the top of the list of potential quarterbacks in next year's draft are players like Josh Allen of Wyoming, Josh Rosen of UCLA, and Sam Darnold of USC. A recent "super-early 2018 mock draft" published by Jared Dubin of CBS Sports has those three quarterbacks making up the first three selections of next year's draft – in that exact order.
Using CBS Sports' projected win totals to set the draft order, the 49ers are selecting second overall behind the Cleveland Browns. That puts them in place to make Josh Rosen their quarterback of the future, according to Dubin's mock.
Below is what Dubin had to say about the 49ers' selection of Rosen:
"Brian Hoyer is a nice stop-gap option for the 49ers, but if they wind up with another top pick in a QB-heavy class, it seems safe to bet on John Lynch and Kyle Shanahan taking the plunge."
Rosen, who beat out Jerry Neuheisel, was named the Bruins' starting quarterback in 2015 and was the first true freshman in school history to start a season opener at the position. Rosen finished the season completing 60-percent of his passes for 3,670 yards, 23 touchdowns, and 11 interceptions, earning him the Pac-12 Freshman Offensive Player of the Year award.
Rosen's 2016 season was cut short due to a throwing shoulder injury suffered in October against Arizona State. In seven games, he completed 59.3-percent of his passes for 1,915 yards, 10 touchdowns, and five interceptions.
Of course, a lot could happen before the draft. The "nice stop-gap option" whom Dubin referred to when describing Hoyer could surprise and thrive within Shanahan's offense, leading the 49ers to a better record than most expect. That might take the team out of reach of the top three spots in the 2018 NFL Draft. One of the projected top three quarterbacks might fall due to unforeseen circumstances during the 2017 college football season. Another prospect, much like Mitch Trubisky of North Carolina did prior to this year's draft, could emerge as another legitimate candidate for a top selection.
We have a long way to go until the 2018 NFL Draft, but it remains likely that the 49ers will be targeting a top quarterback next offseason – draft prospect or otherwise – as the team continues its rebuild.