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At the end of Terminator 4 Kyle Reese ends up in the terminator factory. But instead of killing him Skynet runs some experiment on him (?). Or is Skynet trying to turn him into a terminator? It's too bad the "surgeon" terminator is interrupted by the girl and we don't get to see the whole operation.

What exactly is going on in that room?

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In Terminator: The Sarah Connor Chronicles, the episode from season 2 called "Complications" has a few scenes which is similar to the one you speak of with the "surgeon" terminator. In these scenes, Charles Fischer shows an audience of terminators interrogation techniques to get information from captured resistance fighters. Because the little girl doesn't talk, the machine may have logically determined she was trying to be tough and would not divulge any information. We may have witnessed the beginning of an interrogation.

The room in which Kyle Reese was held was likely just a holding cell. He was simply bait used to lure John Connor into a trap. Turning Kyle Reese into a Terminator would be much more complicated to do in such a short time as opposed to laying a simple "I have to rescue my father" mission. The T600 that comes to his cell may have been sent to terminate him, or relocate him to another part of the facility for interrogation as well. He is a member of the Resistance as well, and there could be valuable information that could be learned from him while he is alive. (Explanation for strike out here)

If Kyle Reese is killed, John Connor would still remain in existence because a Kyle Reese from another alternate future was sent back to protect Sarah Connor as evidenced by Kyle Reese traveling back in time from a future where Judgement Day was August 27th 1997, however in Terminator Salvations Judgement Day was sometime in 2004 (http://terminator.wikia.com/wiki/Judgment_Day).

John Connor is the biggest threat to SkyNet after he becomes the leader of the Resistance. During T:Salvation, he is just a commander and of little immediate threat to SkyNet. However, SkyNet is aware of his future abilities and terminating him prior to his ascension to that post is what really matters to SkyNet.

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So the "operating table" where Reese lies is really an "interrogation table"? I guess it could make sense. –  Arne Evertsson Aug 27 '12 at 10:31
    
In response to another question about the same part of the movie, I came to the realization that Kyle Reese likely wouldn't be killed by SkyNet. I have updated this answer by striking out the possibility that the T600 was sent to terminate Kyle Reese and linked to the other question for reference. –  TexasTubbs Nov 14 '12 at 21:28
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In the original script, they were intact literally removing brains and putting them into terminator bodies, Kyle Reese and all. Not saying that's what was going on in the final movie, but it seems like whatever was going on was half baked due to rapid script changes. I think it was said in the film that they were capturing humans to experiment on them tho... Not to confuse the table scene with the scene with the holding cell, where the t600 shows up to take Reese to the table. Idk what experiment a Gatling gun equipt 600 would perform tho, again, it seems half baked.

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