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When Quaritch was in his AMP suit and smashed the window of the link station, Pandoran atmosphere leaked in, spoiling the integrity of the air in the trailer. Jake was finding it impossible to keep linked with his avatar because of the alien air he was breathing and, after climbing out of the link, he was on the brink of death. Yet, after Neytiri killed Quartrich and revived Jake's human body, somehow, Jake is able to return to his avatar's body because the next time we see him, he and Neytiri are at Tsu'teys side.
Was the link able to function in Pandoran atmosphere? Would it be possible for human Jake to use an exopak in the link to transfer to his avatar? Can the equipment in the link conform to an exopak? Don't the electrodes (or whatever they are called) need clear access to Jake without an exopak in the way? Was Neytiri able to operate the link while Jake was in it? How do all the pieces fit together? Or do they? ;-)