Let me just say first that despite the fact that this post will dismember the movie, it was very good and very well-realized. The spaceship at the beginning is a rod with spheres and centrifuges -centrifuges!- attached. It drops spaceplanes rather than landing. The marines act like soldiers. There is a hell of a lot of life on Pandora, much of it sort-of implausible but all nicely designed. The bird-things use a unique wing structure, amazingly*. One part that struck me well was that all the vertebrates have a similar structure: two back legs, four front legs, tiny secondary eyes, frontal snouts that kind of fold the jaws into each other, two tentacle-ear things that hold the nerve-bundle endings. The obvious exception is the Na'vi, which are gratuitously humanoid; but early on you see this lemur-like primitive primate, which has vestigial secondary arms, almost nonexistent secondary eyes, and frontal main eyes, a flattening snout and quasi-nose. Even though they couldn't or wouldn't make the Na'vi as inhuman as the local body plan seems to demand, they nevertheless figured out a developmental path for humanoids and even put it in the movie to be seen if you want to bother looking.
So: plot holes to fill. We'll do a little one first, before obvious disaster #1: They need an Elevator. They're moving bulk resources, they have spaceships, a Space Elevator is a necessity. Admittedly, they're still out of current materials-science reach, but so are the spaceplanes they use, and people are going to stop laughing at the concept within a decade of them becoming common movies, just like rockets in the 1920s and 30s. I still can't think of a movie with an Elevator in it.
Now, the big one: Unobtanium. Ungh. In The Core, they had unobtanium, but when that movie introduced it, you could hear the writer telling the audience: "Look, for the plot we need a plot device. Here it is. I know it's a plot device. Let's move on quickly." In Avatar, they move on just as quickly, but the implicit admission of MacGuffinhood by this movie gels far less well. Another option we saw might be to just have it be iron or tungsten or something, which would be less jarring at the cost of painting a far grimmer picture of the resource situation on Earth. (I have since found out that the unobtanium is room temperature superconductor, which is why the piece in the main office floats, and why the Hallelujah Mountains over the sacred tree and its big EM field float, and why its so valuable. That, said, I still think my idea is neater.) But there's an even easier solution: biologicals. We're already searching our disintegrating rainforests for chemicals and production methods, an alien jungle world like Pandora would be a goldmine far exceeding any rocks you could haul out. (Not to mention, unique biologicals will always make more sense to go space traveling for than bulk metals.)
The swap of "unobtanium" for alien biologicals tightens up one small but oh-so-glaring flaw in the movie, but if you follow the train of logic it really makes a difference to the movie**. First up: the Avatars. So humanity has this make-a-new-body technology, which (since the original has to still be alive to function, isn't quite immortality) but still seems pretty game-changing to me. David Brin wrote a book, Kiln People, about the effect this one technology alone would have on society. Also, towards the end it becomes clear that the Avataring tech synchs nicely with the preexisting Pandoran neural-interface tech. So why not have them linked? The Avatar technology isn't an unrelated feature, it's the first big dividend the planet has paid and we're trying to find out if it has more.
Form here, in turn, you can tighten (or at least rejigger) the character set a little too. In the original movie, there are three groups of humans: scientist, soldiers, and suits/miners. the last is largely superfluous in the ore plot, and can be dropped entirely in the biologicals one. (The fact that the only speaking suit or miner is Burke, who I've renamed out of laziness after an identical character in a 20+ year old movie says something about their contribution to the plot.) So now we're down to the scientists and soldiers, and instead of a giant industrial base we have (let's say) a little prefab compound at Elevatordown, and that's it. The Na'vi don't have the original reason to fight the humans (although if you want to stop here you could easily splice in something about the Na'vi home-tree secreting or containing something blah blah fight scene.)
All right - here's two more things from the movie to add in. Jake goes native far more than any other Avatared scientist ever has, but he also is linking with the animals (and thereby the Planetmind) far more than anyone ever has. Possibly, if dubiously, he is the first to do it ever. Now, I'm not suggesting he gets brainwashed and reprogrammed (although that makes for one hell of a dark possible interpretation) but he's way more in tune with it than anyone else. So why not take this and run with it? Also - it bugged me how human the Na'vi were. They were biologically weird, but despite this they thought a basically like people - give some New Guineans a holistic nature spirit that responds like the Planetmind does and they'd be indistinguishable, culturally. The most glaring example is Jake's initiation ceremony: it looks pretty generically tribal, despite the fact that they can link minds with stuff and it has been demonstrated linking is not even as personal as sex to these people, and this is obviously the most complete and biologically sensible initiation ceremony, they don't link up with him.
So let's take these points about linking and the Planetmind and go with them. The Na'vi can start to be smart like people without thinking like people because they no longer are people in the complete sense. They are sentient, yes, and individuals, but their culture is literally inhuman because it revolves around things people can't physically do and can barely comprehend on an academic level, once they figure out what's going on at all. And the Na'vi are always in low-level contact with the rest of the ecosystem and the Planetmind - this last is already implied a bit by the movie. Now, when the humans come down, the first encounter-suited guys are going to weird the heck out of the Planetmind***, since they're not connected or related to it at all. The Na'vi, when the humans run into them, are going to be incomprehensible: they sometimes act like reasonably human hunter-gatherers and sometimes are totally alien. One Na'vi will meet a party and be entirely docile. Another will meet the same party and, because one of them stepped on a beetle thirty seconds before and the whole forest has suddenly tensed up, will murderize them unprovoked. The first will agree, on later encounters, that the party were all fine fellows, and at the same time that the second's attack was also entirely fine, on the basis of sub-subconscious feelings that neither can explain or understand why they would have to explain.
As this goes on, some scientist figures out a fraction of the neural connectivity of Pandora and figures out an Avatar-making process. They test it and it works beautifully: they have a human inside a Na'vi body, but it doesn't work on non-Pandorans (they can't do human to human, which is obviously what they would want) and even worse, it doesn't work off-planet. They can gat all the obvious parts set up but without the permeating and enabling Planetmind (which no one knows about or has even really imagined yet) nothing moves. So they now have this Avatar system, which think they only barely understand and don't really understand at all, perfect for exploring the planet and (on encounter with the Na'vi) something the Na'vi trust to a degree that makes no sense (even when the Na'vi know it's really a human they trust it almost implicitly). They start using it.
Now the crazy-fun begins, because once people start wearing the Avatars, they're in contact with the Planetmind too. Because they're not really Na'vi they don't go quite as far as the real Na'vi do in acting on it, but Avatar-drivers start to develop what look like psychological problems after a while: they start getting erratic and emotional - more, they start getting emotional weirdly, having increasingly incomprehensible reactions to regular events. After a very long time, they start losing rational reasoning ability - they still think, but in ways that look schizophrenic to normal humans. Cycling them out, to everyone's great relief, brings quick recovery, but putting them back in an Avatar in turn brings immediate relapse. The people in charge figure out a "safe time" - probably somewhere between weird emotionalism and the complete "schizophrenic breakdown" and start cycling people through. Figuring this out is still obviously valuable enough to cover some temporary psychological disturbance (certainly all the volunteers think so).
At this point, enter hero.
*For reference - each time vertebrates have evolved flight on Earth, they built the wing slightly differently. Bats stretch membranes between the fingers. Birds hang feathers off a simplified arm. Pterosaurs hung membranes off the arm and lengthened fourth finger, with the other fingers a tiny claw halfway down. The Banshees in Avatar use pterosaur-like arm/fifth finger arrangement, except the other four also extend out to form little adjustable surfaces at the outside edge.
**Not least, which is probably why they didn't do this, it shoots the message in the head. The strip-mines, hauler trucks, and industrial plants that show up early on form a pretty impressive visual contrast to the eco-friendly Na'vi, and backs up Cameron's Industry V Nature theme beautifully. My McGuffin doesn't allow this and by the time it graduates to the status of plot point down the article a bit, the theme is more Man and the Alien anyways. Which is a nice theme which (surprisingly few, given their ostensible subject matter) sf films do, but it's not Cameron's point.
***In the movie it's never made clear whether the Planetmind is sentient - you can read the evidence plausibly either way. My personal preference is that it isn't - it's smart in an inhuman fashion, but isn't what we would think of as conscious. The Na'vi are, but as individuals, not as part of a larger conscious entity.
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