The destruction of Cyberdyne Systems at the end of Terminator 2 does not quite send everything back to the starting point. Although Cyberdyne was very secretive about its research, it was holding a position as a defense contractor working on the SkyNet project up to the moment it was demolished, and it undoubtedly fed some of its research data to the overseeing agency, the United States Air Force, Autonomous Weapons Division, Cyber Research Systems branch. The hardware is gone, and Cyberdyne has nothing left of its work, but the Air Force has copies of at least some of the material. It will never build that computer that was envisioned; but it will use some of that information to advance its autonomous weapons systems, creating those devices we see in the third film.
So if the presence of those super weapons in a story set in 2004 snapped your disbelief suspenders, you should take heart that it was not the original version of 2004 you were watching, but an altered version created by multiple trips from the future. There would have been a previous timeline in which such systems were never developed so early. The original software version of SkyNet also was not so powerful as the one in the film; it did not have the advantages of Cyberdyne's earlier research.
However, it did come on line, probably in or around 2004. It was a software solution launched against some sort of virus crisis on the Internet, and it interacted with the virus to create an artificial intelligence. Almost immediately it declared war against humanity, perhaps to terminate us before we terminated it. It also led to the development of killing machines, one of which was sent to the past on an unsuccessful mission to kill Sarah Conner, resulting in a shift as Cyberdyne got the materials to build a better system sooner. Then Sarah swept away Cyberdyne's work, leaving only a residual advance that returned history to the creation of SkyNet on the original schedule, the replay of the previous interwoven time trips, and the sending of the T-X to kill a long list of targets, leaders in the rebellion.
History is certainly complicated at this point. All that has happened already has to happen again, in much the same way. Cyber research will escalate with the discovery of the T-800 parts in Cyberdyne's machines in the past, and then crash with the destruction of it all by Sarah Conner. However, to this point history can stabilize, and we can proceed to the next temporal event. That event is the sending of the T-X by Skynet, followed in yet another event by the sending of the T-800 by Kate Brewster Conner, and will require a full treatment to unravel. There is, however, another complication in the third film before that one: if there is no T-X, how do we reach the place where John marries Kate? That will be considered next time.
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