I think the explanation was that in the future, the robots had already lost the war, so killing John Connor then wouldn't make any difference. So they went into the past to kill him before he could lead the humans to victory.
Yeah, that's the back-story.
What I still don't get is, in the first movie Michael Biehn explains that he arrived through the time portal naked and unarmed because only living tissue can go through. "Nothing dead goes through." When asked to explain how the Terminator was able to get through, he explains that it is "covered in living tissue." Okay, I'll buy that. But then how do you explain the T-1000, whose body is made entirely of liquid metal? He is NOT covered in living tissue. Living tissue is nowhere a part of the T-1000 design. He is merely able to mimic the look and feel of living tissue, but it still is NOT living tissue.
And, furthermore, anyone else bothered by the fact that the Schwarzeneggar-bot in Rise Of The Machines claims that "psychology is one of [his] sub-routines"? Uh, what?!? Sure, there were LOTS of things wrong with Rise Of The Machines. I mean, as a whole it was a BAD movie with a capital "BAD." But, seriously, there's a scene where the Terminator tells John Connor, who is lamenting his situation, basically to go screw himself, which makes John Connor p**sed, and the Terminator tells him to use that rage to his advantage because "anger is more useful than despair" and explains that he knows this because of his human psychology programming. Excuse me? This thing can spit out "anger is more useful than despair" but, as we see in T2, he doesn't know what the hell crying is? What the hell?!?
Bah, whatever. I'll see Salvation when it comes out, even though it'll probably suck. I've always wanted to see more of that post-apocalyptic future war, but I'm sure they'll screw it up. As promising as the possible stories you could tell are, they're probably better off left unexplored on the big screen. When it was just T1 and T2, the future kept an element of mystery that let you fill in the blanks and let your imagination run wild with what the future could be like. It was intriguing. With Salvation, what'll end up on-screen probably won't be half as cool as what has been bouncin' 'round in the brains of the fans of the franchise ever since the first flick.
First flick was great. Second was near perfect (with the exception of some plot holes, like the one mentioned above, and the absurdly saccharine, eye-rollingly trite ending: "if a Terminator can learn to appreciate human life... maybe we can, too" ...::vomit::). Third was terrible. This fourth one? It'll probably be better than no. 3, but that ain't exactly hard. It'll probably still suck. Hard. I lament the fact that the early rumors of Josh Brolin ending up in the movie turned out to be worthless. He's a great actor (I'm extremely happy that his career has recently seen such a huge resurgence in the public eye thanks to Grindhouse, No Country For Old Men, and, as of late, W.). Helena Bonham Carter is great (and mouth-wateringly sexy) but Tilda Swinton (who was originally gonna play the role Carter ended up filling) probably would have done a better job. And Common has proven himself to be a surprisingly good actor. But Christian Bale sucks. Period. He just sucks. In Equilibrium he played a character with no emotions, and he couldn't even do that well. The best performance he's ever given was in American Psycho, but that only works because the character is so plastic, fake, and over-the-top (just like Bale), and The Machinist was good, but not because of Bale's acting. As John Conner, I'm sure he'll do a lot more of his "look at me, grrrr, I'm angry and tough and mean, look at my sucked in cheeks and furrowed brow, grrrrr" B.S. that I've seen from him enough already.
Let's jsut hope he leaves that horrible "I'M BATMAN... AND I NEED A LOZENGE!!!" voice at home. Ugh.