That's pretty much what happened in the game Deus Ex. The main character J C Denton turned rogue after an assassination assignment at an airport. The government activated a killswitch (24 hours before his nanites eat his brain) and he eventually managed to save his life through a black market machine owned by the Chinese Triads.
Soon after that the main character found a device that could give him the ability to either A: Have his own internal respirator or B: Protect his lungs and indeed the rest of his body from toxins and radiation.
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As for the lack of cyberbreath? I think the only place where you can suffocate is in a few missions in GH2.
It would be a nice addition...
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Quoting: Varil
Anticheese : So....if you met a guy who had cybernetically enhanced his muscles, would you think 'formerly disabled' or 'can kill me with his bare hands'?
True point. I only ment to say that disabling most cyberware components would be fatal to the person involved. Imagine if your heart or muscles stopped working?
Come to think of it there is no reason why the game can't just say: "We don't want you in this base. Your security pass will expire in 60 seconds." to characters that are just visiting or post an armed guard to the character and put movement on railroads.
Sorry for the late reply.