Events changed by the arrival of the T‑1000
Notes on Chronology 4
We must find a way to explain how the T‑1000 failed in its mission to kill John considering that there was no T‑800 there to help.
Keeping as close to the stories as possible we know that John has gone off with his friend to the Galleria. The T‑1000 finds John in the arcade and John runs off. In Judgment Day John is getting away from the T‑1000 when he encounters the reprogrammed T‑800. This causes him to stop, turn around and run back the way he had come. At that point, the T‑1000 shows up.
However, in this chronology no reprogrammed T‑800 is going to arrive. So we have to conclude that John manages to successfully run from the T‑1000. Failing to catch John, the T‑1000 then goes to the foster parents' house, kills the mother and awaits John's return.
We must also realize that John does not know this is a Terminator. All he knows is the police are looking for him, probably because of his stealing money from the ATM's. At some point in the evening John probably calls his foster parents, perhaps to see if the police had been there or are still there. His foster mother's behavior on the phone is odd and he becomes suspicious. He may only be suspicious that the police are there waiting for him and she is just lying. However, he does hear the dog barking in the background.
Eventually John returns home most likely sneaking into the backyard to see what might be happening and notices that the dog is dead. This must make him really wonder what the hell is going on. Obviously if the police were after him, they wouldn't kill his dog. At this point the memory of dogs and Terminators may come to mind.
He sneaks up to the house and looks inside. He sees his foster father dead. He also sees his foster mother.
We do not know what happens at this point. Does John see something that makes him realize that a Terminator has arrived? This is unlikely as Sarah's descriptions of the Terminator would not include their ability to mimic the physical appearance of other people. Does he just think that his foster mother has gone mad? Does he try to go and see Sarah? All that we can really be certain of is that John leaves and manages to evade the T‑1000. Perhaps he goes to be with Enrique or returns to Mexico.
When Judgment Day occurs in 1997, John would go through the same revelations we outlined in the Notes to Chronology 3 regarding his loss of faith in his mother.
Now let's look at what might have been going through John's mind at the point he decides to reprogram a T‑800 and send it back to 1994. We do not know whether or not John ever found out or figured out that the events that had taken place back in 1994 were due to a Terminator. Regardless, finding out now that Skynet has sent a Terminator back to 1994 to kill him makes all of those events make sense.
John realizes that he has no idea what effect on the past Skynet's actions might have. He could have been killed back in 1994 and never even known it was Skynet. John decides to end this once and for all. He reprograms a T‑800 and sends it back with "detailed files" on Myles Dyson and Cyberdyne. Obviously in an attempt to prevent Judgment Day.
We must note, Kyle told Sarah that Judgment Day would happen in 1997 and it does, John does not know that events have already been changed. All he knows is that Skynet is attempting to change the past and, uncertain of the effects this might have, he makes the decision to terminate Skynet.