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Towards the end of Season 1, David Robert Jones shows up at the FBI and demands to speak with Olivia Dunham, during the conversation she says something that implies he's going to die as a side-effect of teletransportation but he answers:

"I never said I was going to die, It's much worse".

In the season finale, we see him covered in bandages, bullets cross right through him (that's what he says to Olivia) and one of his eyes has turned white. To my knowledge, it was never fully disclosed so what exactly were the side-effects that he encountered?

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  • I have a vague memory that Walter explains it in Season 4 – Izkata Aug 26 '14 at 3:46
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Sine the teleportation device was not perfect, it caused Jones to become unstable at a molecular level. This would definitely cause gaps within the body, which would result in infections, damaged skin and so on.
Another proof of this molecular instability is his apparent invulnerability to bullets. If his molecular structure itself was unstable, there is a good chance the bullets might go through him without causing much damage.

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