First of all, I want to say that I know that all this is about a work of science fiction. The use of temporal loops in science fiction is always to invoke a little wink, wink, nudge, nudge to the reader/viewer. Temporal loops can't be solved. They will always imply a theory that can't be proved or which another theory will contradict. They are clever, (or not so clever) plot devices designed to make the viewer/reader think "Oh, so that means...” but only for a second or two. If you think about them too much, you end up here, trying to make sense of anything Saberist writes.
Having said that, there is one way to relive yourself of the "Kyle Reese is John Connors father and what about Cyberdyne/Skynet" headache.
Chaos Theory. It states that the future is made up of the sum total of all decisions that anything that can make a decision makes. That would be the future five minutes from now, or five hundred years from now. Every second of the day, we all go along making decisions to do this, or to do that. Assuming that no “thing” can affect how you make a decision, the idea of fate or destiny is disproved. If nothing can control our thoughts, and the decisions we all make determine the future, then the future is never a set outcome. The future is, literally, only the next second away.
In the Terminator series, the biggest problem is the idea that Kyle Reese is destined to be John Connors father. There is also the idea that Cyberdyne/Skynet was born out of them finding the pieces of the original Terminator. This implies that the temporal loop that brings the first T-800 back to 1984 was destined to happen. Chaos Theory says this is not the case. We have never seen the FIRST timeline.
If you let the idea that Kyle Reese is not John’s original father, and that Myles Dyson was not the primary scientist to develop the advanced microprocessor the first time, then those nasty little time loops go away. Anybody could have been John’s original father in the first timeline. Instead of meeting Reese that night, she might have had a one-night stand that left her pregnant. All Skynet knew was that the son of Sara Connor would lead the revolution.
Just because Thomas Edison invented the light bulb, does not mean that someone else would not have. He was just the first. Any one, or many, of the engineers at Cyberdyne could have developed the technology that led to Skynet. This is what could have happened in the first timeline.
The first timeline ceased to exist the instant Reese was sent back, and the SECOND timeline began when he arrived in 1984. The events of the first Terminator make up the second timeline. Reese fathers John Connor, they defeat the first T-800, Cyberdyne gets the pieces and then Myles Dyson develops the chip that lead to Skynet. This timeline allows the events of T2 to happen.
It could be said that with the advanced jump in technology that the first T-800 gave Cyberdyne, is what led to the T-1000. (If the T-1000 existed in the first timeline, Skynet would have sent it.) It could be said that all technology is advanced a great deal because it is in the second timeline that the rebels are able to “capture” a T-800 and send it back to protect Connor. If they could capture T-800’s in the first timeline everything would be different. The second timeline ceased to exist when the T-1000 and T-800 are sent back and the third timeline begins in 1991. In T2, they think that they have destroyed all information and hardware that leads to Skynet. Well we can see that they didn’t and since I am getting tired of writing, we can see that the third timeline ends and the fourth begins with “T3”. All timelines are discreet and do not loop or overlap. Problems solved, now go watch something like “Finding Nemo”.
Dr Plaid