Question: The ending of this film seems rather vague on the actual outcome of destroying Skynet's HQ. Does that mean the humans have won the war or is Skynet still a threat? The ending of Terminator 3 would suggest the latter since there it was confirmed that Skynet is capable of moving from transferring itself from one installation to another when needed, yet here everyone seems to believe they accomplished a significant victory. So which is it?
Question: Why would Skynet want to kill Kyle Reese? If he doesn't go back, he won't destroy the first Terminator, and that arm will not end up becoming Miles Dyson's inspiration for creating Skynet (as stated in T2), and if Skynet isn't created at that point, they will never exist in the future. Surely the machines would work this out, and make sure the loop is completed (i.e, not killing Kyle so Connor can send him back?
Question: Why did the T800 near the end destroy the 600 that was experimenting on Reese? It just seemed to be a bit out of "character" for the Terminator to unnecessarily kill one of its own kind.
Question: When Marcus goes to Skynet he is "analyzed" by the large machine, that recognizes him as being a machine as well, and then he is granted access. So why did the Terminator not recognize him as being a machine and try to shoot him earlier in the movie when he first reaches the city?
Question: One burning question: Why do the machines need to capture the humans? What do they need them for? Surely a neurotoxin introduced to the atmosphere or water table would eradicate all non-mechanical life?
Question: John Connor knows about the future because of the experience he had with the Terminators sent to kill him and the tapes his mother left him. But what about Skynet? How does Skynet know who Kyle Reese and John Connor are and their importance on the future? How does Skynet knows that Kyle Reese will, or has, become John Connor's father? Because that isn't happening in the future, but in the past where Skynet didn't even exist.
Question: Why would the Skynet base where Connor obtains intelligence in the beginning have human friendly computers - i.e., computers with keyboards? Skynet does not need to type and look at a monitor, but can just communicate computer to computer.
Question: The commanders said that the destruction of Skynet in LA would end the war but when John blew it up, he said the war is not over. Did the commanders mess up on that statement or what?
Question: When Dr. Kogan is meeting with Marcus, she gets Marcus to sign over his body for research following his death. Later in the film, Marcus discovers that he's been turned into a cyborg. Why did she do this to him and what did she hope to accomplish from it?