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In Terminator: Genisys, we are told that the time machine destroys anything metal.
However, the time machine is used as a weapon against John Connor at the end because he is metal. So how does he travel through time earlier in the film if the time machine would supposedly kill him?
It is made extremely clear in the film that anything — even metal — encased in flesh can be sent back without harm using the temporal displacement device.
In the first instance when John Connor travels through time, a layer of flesh is presumably intact around his magnetically-arranged metallic components. (This is not shown on-screen, in order to set up the twist that John Connor has become a type of Terminator, the T-3000). The T-3000 is, in a sense, a virus that has infected John Connor's body, partially reconstructing it, but preserving his memories, consciousness, and some of his flesh. It seems to be able to assemble and reassemble this flesh at the cellular level, along with its metallic components.
Indeed, the
Villains Wikia describes the T-3000 as a "hybrid nanotechnological human-cyborg". The T-3000 himself proclaims, "I'm not man, not machine. I'm more."
At the end of the film,
there is no flesh around these components as a result of the fight with "Pops" (the Terminator protecting Sarah Connor) who was using magnetic "brass knuckles" to disrupt the T-3000's magnetic scattering control. This is why the T-3000 and the displacement device are subsequently destroyed.
It's not explicitly stated, but the most likely answer is that the the character had a flesh covering for their initial trip back in time, then shed it when it was no longer useful. We could make the same assumption about the T-1000s. A living flesh covering isn't particularly useful when you can shapeshift at will, and don't plan on time travelling.
Since John Connor's exposure to the incomplete time machine at the end of the film was unplanned, and he was shapeshifting like crazy up into that point, it stands to reason that any flesh cover he may have previously had would've been dropped or shredded.
In addition:
Since John Connor was human prior to his transformation, it's possible that Skynet just didn't fully convert the outer layer of his flesh, since it was planning on sending him back in time immediately. Then, it would've been shredded as soon as he shapeshifted some clothing upon arriving in the past.
Those are just my guesses based on the available evidence. It's also possible that the incomplete nature of that particular time machine had something to do with it.
