It seems odd at first glance that John Conner and Kate Brewster should meet and marry in that history that flows from the end of Terminator 2: Judgment Day. After all, no T-X is going to appear to kill Kate, and no T-800 will arrive to save her, so why does she not marry Scott?
It first must be recognized that Skynet did not launch the virus that led to its own creation. While such a predestination paradox would have been the sort of thing time travel movies like to do, there is no evidence to suggest that Skynet did this. Rather, it seems to have targeted this moment because it was aware that it was about to be created, and it sent a terminator back to take steps in preparation for that. This is important, because it means that the virus will invade the Internet, General Brewster will launch his experimental SkyNet defense against it, and SkyNet will be born in very much the form we see in the film.
It also must be recognized that John Conner's actions between the end of Terminator 2 and the beginning of Terminator 3: Rise of the Machines are not going to be altered by anything SkyNet does in this film. He drops off the grid and keeps moving. There is every reason to believe he will have his motorcycle accident at the same time and place, and that he will burglarize that veterinary clinic looking for antibiotics. Betsy's cat likewise will get sick on schedule, and Katherine Brewster will report for duty at the clinic to treat it. There she will meet and cage John, recognize him, and possibly (in the absence of the crisis) take him for breakfast.
He will tell her that he did not kill his foster parents, but that the person who killed them was trying to kill him and might still be pursuing him; that this is the reason he vanished. He will not yet mention machines from the future, but he will say that his mother knew, and that she, too, was on the run. As to why this is happening, he will probably hem and haw a bit.
By the end of breakfast, the virus will already have begun its work. Cell phones and credit card services will crash. General Brewster is preparing to launch the program. John Conner, however, is already paranoid. He will beg his old friend to drive him away from the city, probably to Mexico, because he is anticipating the disaster he still believes is inevitable. With no T-800 to mention the role of General Robert Brewster, John will not make the connection to Kate. He will offer her whatever money he is carrying, certain that it will be worthless in a day or two anyway, and she will agree, because she really does like him even though she thinks he's a bit crazy, and John Conner is nothing if not persuasive.
Before they reach Mexico, the missiles will have been launched. Scott and Kate's anticipated future is reduced to ashes. John and Kate are thrown together in a desperate bid to survive. Eventually they will return here and find the rest of the resistance; for now, they are on the run.
Kate now becomes a threat equal to John. SkyNet knows where she was that morning, and so sends a machine back to kill her and a number of other people. That changes history again, which we will consider next time.
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