Apparently, when they filmed the ending for this Season’s finale of Jericho, they filmed two endings. Via TV Guide:

TVGuide.com: Will viewers have any burning questions coming out of the alternate ending/series finale?

Carol Barbee: Let me see…. I can tell you that in the original ending, Hawkins has to sacrifice himself to let Jake get away with the bomb and get it to Texas so it can be tested and prove that they were telling the truth. Texas would then swing their support to Columbus and defeat Cheyenne.

Carol also said:

TVGuide.com: Does Hawkins mortally sacrifice himself, or just let himself get captured?
Barbee: Well, he gets captured but he’s also shot…. He’s pretty messed up, and Jake feels like he’s leaving him for dead. So we show you where he’s taken and you see that the mission for the next season is, “We have to go rescue Hawkins and we have to stop these [bad] guys.” When they see the alternate ending, it certainly completes the story from this season and tells you everything you need to know to have understood Season 2. It just doesn’t point to that next mission. You meet John Smith, the guy who’s been pulling the strings. It’s [played by] Xander Berkeley (24). You’ve heard him on phone calls, and Hawkins is surprised by who he is and where he is. So you know who John Smith is, you know who planned the attacks, you know why, you know how….

Both endings are good, but the new ending definitely wraps things up a little better. The original ending would have left us wondering what in the world was going to happen to Hawkins. I was very happy with the ending they came up with. I hope that somehow Jericho lives on, which brings me to…

From what I understand Jericho did get decent ratings, which means that it could get picked up by someone else (especially a cable station). I will go ahead and my cross fingers on that news…