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If Kyle was the father of John... and he was the father because he came back in time to help save Sarah... How was there ever an original John to begin with that fights the machines and sends kyle back in time? To go further.. how would Sarah train john a war she knew nothing about.. she only learned what was going to happen when Kyle came back? This has always confused me and I'm not sure if they ever answered it in the movies.. Thanks

John had a father other than Reese before the loop began. If you notice, where John came from is a mystery to Reese, it could be intentional (obviously), but it could also have a deeper meaning, his father was someone else. Who knows, maybe his original father was the douchebag boyfriend Sarah cheats on.