Two thoughts on this:
With the RDA out and hopefully not returning, there could be a science community established as link between Earth and Pandora. Hell’s Gate could be a University extension site of sorts. The base could be dismantled of its Military and Industrial components and those wishing to study the planet would be allowed to come in. This could be one scenario.
The scientists left behind would most likely begin cloning Avatars for those who do not have them. These people could then slowly integrate into the Navi communities as Jake did. It would seem that the technology is there and that the Base would sustain itself for some time with minimal preventive maintenance.
The weapons in the jungle, even if you could find them in the brush, would likely rot and disappear.
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