49ers hire Chip Kelly, so what happens to Colin Kaepernick?

When news broke that the San Francisco 49ers were down to Chip Kelly and Mike Shanahan as their head coaching finalists, one thought emerged: They're not ready to discard Colin Kaepernick.

We shall see if that proves to be true, but when the 49ers announced Thursday that they had hired Kelly, it stirred the imagination of what could be with a rare talent at QB and a creative offensive mind.

Kelly was fired one game prior to the completion of his third full season with the Philadelphia Eagles, earning an overall record of 26-21 with two 10-win seasons and one playoff appearance (a loss in the wild-card round to the New Orleans Saints in Kelly's first season in Philadelphia). But tensions arose after Kelly earned massive power in the organization and started making personnel moves that confounded players, fans and people within the organization alike.

Still, despite not having a great talent at quarterback in nearly three seasons with the Eagles, Kelly's offenses ranked third in points per game (26.9) and total offense (392.8 yards per game), and fourth in rush yards per game (131.3). Perhaps working with a player such as Kaepernick — even though Blaine Gabbert proved to be more able by the end of the season — was the allure for the 49ers in Kelly, and him in them.

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Kelly's biggest mission could be to break down the broken Kaepernick, who was benched in November after an ineffective and injury-addled 2015 season on a 49ers team that was decimated by player losses, and build him back up. Is it a guarantee Kaepernick will be back? No, as perhaps Kelly's work with middling talents with the Eagles is proof that he doesn't need that kind of player. There's also the matter of Kaepernick needing to be built up physically, coming off three surgeries (left knee, left shoulder, right thumb).

But on the other hand, there were enough rumors that Kaepernick could be released by the 49ers and join the Eagles in 2016 assuming Kelly was going to be back next season — how about that — that we assume this could work with the 49ers, Kelly's new team, even if Gabbert can't be eliminated from the equation.

The 49ers still should be in excellent salary-cap space for next season, with somewhere north of $40 million in room and perhaps as high as $50 million with a little belt tightening. So that would appear to eliminate the  need to cut a 28-year-old quarterback whose cap hit would be less than $16 million, or a shade over 10 percent. That's hardly unwieldy at all. An offense that averaged 14.9 points per game — dead last in the NFL and nearly a field goal below than the next-worst team — needs all the offensive talent it can get its hands on.

The 49ers do not have the personnel talent that the Eagles did but they have reliable pieces such as Joe Staley and Anquan Boldin on offense, defensive pieces to build around in NaVorro Bowman, Ian Williams, Eric Reid, Aaron Lynch and Jimmie Ward, among others. Perhaps having a solid defense in place can help allow Kelly to develop his offense over time and figure out if Kaepernick is part of the solution there. The team also has players in Carlos Hyde (if he's healthy) and Torrey Smith who could help flourish in this system under Kelly, and the seventh overall pick in the 2016 draft could net them an immediate impact player.

It felt odd that the 49ers would go back to hiring a coach whose best work came at the college level considering the way things ended with Jim Harbaugh, but the biggest question —raised last week — would be the relationship between general manager Trent Baalke, owner Jed York and Kelly. Harbaugh sparred with the 49ers' front office, and his relationship with Baalke dissolved by the end of his tenure. Although Harbaugh and Kelly are two different animals, they're both offensive gurus with standoffish personalities who prefer to be left to their own devices.

Is this proof that Baalke and York are admitting their mistake on Harbaugh and willing to let Kelly do his thing without meddling? Has Kelly learned that he perhaps was not ready for such major personnel control with the Eagles and that he should focus his primary energies on coaching? If so, this pairing has the potential to be potent in time. Perhaps Kelly already having a connection with 49ers personnel executive Tom Gamble, who was with Kelly in Philadelphia, could be the proper intermediary to make this experiment work in harmony.

And no matter what happens it's going to be fascinating to watch.

More on 49ers' big new hire

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Eric Edholm is a writer for Shutdown Corner on Yahoo Sports. Have a tip? Email him at edholm@yahoo-inc.com or follow him on Twitter! Follow @Eric_Edholm