Here's what I'm thinking for season 3:
Mitch was saved by a Shepherd and it's the Shepherds who have been holding him captive and making him work for them all this time. Jamie was the one who raised Clementine, and either she's still doing investigative reporting (while also writing books) or she's been encouraging Clem to do the same. Jamie and/or Clem have sniffed out some very interesting (and highly secretive, I'm guessing) research being done in some faraway place and they realize that that research has Mitch Morgan written all over it. Assuming Mitch is being held against his will, he is certainly more than intelligent enough to seed his work with clues to let his friends and his daughter know that he is still alive. Jamie and/or Clem figure it out and Clem sets off to gather the team together to rescue Mitch.
As for why Abe didn't recognize Clementine immediately...well, that was a little silly. I understand that for the purposes of a dramatic season finale, Clem revealing who she was to Abe would be the moment on which they wanted to end. (The revelation that Mitch was still alive would have been a better choice to cap the scene, but they never asked me, so...) So let's just hand-wave it away by saying that Abe and Dariela lost touch with Jamie a few years prior and that's why that happened.
Zoo writers, please feel free to use this. And if this is, indeed, what ends up happening, I will be doing my "I told you so" dance. Just so y'all know.
