I think Harbaugh had his eye on Kaepernick all along, even before he took the Niners head coaching job. Alex Smith was never going to be the future QB for the Niners under Harbaugh. And ironically, you can also give Andrew Luck some credit for scouting Kaepernick for Harbaugh (Both QB's were at the Manning academy). Interesting article regarding all of this: http://www.sfgate.com/49ers/ostler/...-Kaepernick-in-2011-4218962.php#photo-4077921 "If the scouts weren't impressed, Luck apparently was. He and Kaepernick became pals, and when Luck returned to Stanford, Harbaugh asked him if he'd seen anyone who looked good. Oh yeah, Luck said. Colin Kaepernick. Andrew Luck: the Bay Area gift that keeps on giving. In picking Luck's brain, was Harbaugh thinking and plotting ahead one year, to when he might be an NFL coach for a team in need of a good young quarterback? Who knows? Fast forward to the following spring. Harbaugh gets the 49ers' job, decides Alex Smith will be his quarterback for the present, but what about the future? That's when Harbaugh and Baalke head to Reno."