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In 2018, Skynet has Kyle Reese at the top of its kill list. Why?
I first thought it was because Kyle is John Connor's father. But only John and his mother know about that. (Even Kyle himself doesn't know ;)
This element is central to the plot of Terminator Salvation, but I can't remember it ever being explained or justified in any way in Salvation or the other movies.
In Terminator 2: Judgement Day, the psychiatrist in the mental hospital says that John's father is from the future. He also knows all about the concept of terminators. In an attempt to avert Judgement Day, Sarah Connor has apparently not been very circumspect about hiding her knowledge of the future. It is highly likely that she flat-out told the staff at the mental hospital, or one of her other acquaintances over the years, Kyle's name and bio. Even if she did not, it wouldn't take a huge logical leap for Skynet to figure out that if John Connor's father is from the future, and Kyle Reese was the soldier sent back to protect her, then Kyle Reese must be John Connor's father.
Depending on how much of the pre-Judgement Day computer network survives, Skynet may be able to simply check out the birth certificates for every Kyle Reese in existence, then systematically go through them. Kind of like the terminator was doing with Sarah Connors in the first film.
The question, of course, is if Skynet knew Kyle Reese was the soldier sent back to protect Sarah Connor. It's likely Sarah Connor blabbed, but it's also possible that Skynet found out some other way; possibly from the female terminator in the third film.
Actually, according to Terminator Director Joseph "McG" Nichol, Skynet is fully aware of the fact that Kyle Reese is John Connor's father by the events of the fourth Terminator film.
This is strongly evidenced by the fact that Kyle is at the top of its kill-list and by the fact that its infiltration agent (Marcus) seemingly knows that Kyle Reese is John's father.
McG doesn't go into great detail other than to describe it as part of their "recon".
Q: In the earlier movies, Skynet is not aware of Kyle Reese. So, why are they aware of him now?
McG: It’s a function of their recon during the dark period, and a function of their awareness of the events that had happened since Kyle Reese traveled back. By virtue of John Connor being alive, that means Kyle Reese did meet Sarah Connor and impregnate her. That data exists, and was brought into the fold at Skynet.
My personal theory is that since the Terminators are able to communicate with (future) Skynet by leaving time capsules, there's every chance that they've submitted mission reports, images, DNA samples, etc that Skynet could analyse at its leisure.
