Everybody: T4 story line...
...I still haven't gotten over Sarah not being in 3. Unconscionable.
Scene 1, LIFE: So, boy and girl emerge some time later, (1 year, 5 years?) from Crystal Palace obviously with child(s). They have had communications with people in other bunkers and people outside the blast zones, so, there is a loosely organized leadership to get things going, obviously Conner as the head. Because of these communications and who Kate and John are, everyone knows basically what is going on and how dire the situation is.
Scene 2, Learn to Fight: People come out of their hiding places, try to get communites started, find out what parts of the earth are inhabitable, where can food grow and lots of mayhem as the machines stomp on everyone who sticks their head up.
Scene 3, Turning the tables: John and Kate instill the will to survive and win in an otherwise completely hopeless situation. Some people turn traitor and try to sell their fellow man out if the machines will let them live. The machines learn a great new weapon: treachery. Some of these people are engineers who the machines need to advance Terminator technology...and how to perhaps send one back in time.
John and Kate turn the tables and figure out how to start using machines to kill machines and win a huge victory at great cost taking over the main Terminator factory. An ashamed scientist, trying to regain his humanity and make up for his treachery, explains the time machine and what he just helped do and why as he lays dying, noting how little time is left to stop it. Kyle volunteers.
Scene 4, is REBIRTH: Humans begin to re-populate the earth, all the while John and Kate wondering if he will suddenly cease to exist as they have no idea whether Kyle succeeded or not.
The machines are now driven underground and into hiding. No one ever thought to shut down the Bunkers, including Crystal Palace, as these places are now sacred ground. The machines seal themselves in, along with a few more bad humans including a new hero, the son/daughter of an evil genius who has just sent T1000 after Conner. The kid has a human side and thinks of a new/old world instead of the self interest dad engendered.
He tips off Conner about T1000 before going underground with his crazed father and mechanical family and sneaks over the plans of how John to can send a machine to stop this unstoppable assassin. John wants the kid to run away and stay with people. The kid says he has to pretend he still supports his father so he can learn what the machines are up to. The humans have no weapons strong enough to dig the machines out (nukes)and everybody refuses to build anything strong enough. They'll rot in time! The world flourishes!
But, ominously, technology becomes a forgotten skill.
Alas, the machines re-emerge a decade later after it becomes obvious that T1000 failed, organized enough for one last ditch shot at killing Conner in the past; T-X. The humans realize they must nuke the bunkers and send one more T off to the past. Rusty in skill, they screw up, T reverts to old programming and KILLS JOHN!!!
Right before the humans destory this last T while in a rage, Kate stops them. He is the only one they have. They have to program him correctly to send him back.
Before they blow the last bunker up, Kate sends a team down to try and get the kid out. After a blazing battle they succeed, the kid breathes fresh air for the first time in ten years...but he has horrible news...
T5
I finally watched this last night and was pizzed by the way it ended. They should of had a big "TO BE CONTINUED..." scroll across the screen. 
Yep, it is like watching Kill Bill Volume 1 and when the movie ends you stand up and yell "that is it, errrr 
