Big Jim is back—and so is Indy!
The members of the Resistance were able to start over, no longer under the Dome but under new identities. They just had to promise the U.S. Military that they would never contact the citizens of Chester's Mill or speak a word of the things that they saw.
James "Big Jim" Rennie started over with a new position of power, but he would never leave behind his heart! At the end of the finale episode, we saw the Resistance band back together—Indy included!