Here's my idea of how most of the trilogy should go. It's a long post sorry.
Sequel 1: EYWA.
This movie shoud deal very closely with the aftermath of the clash between humans and the Na'vi, but keeping human involvment in the movie at a minimum. Just like the Cold War between the US and USSR, two clans, the Omaticaya and another clan grow dominant. These two clans are not trying to be superior to one another nor do they hate each other in any way, but there is a disagreement. This clan, lets say they are the Na'ring ("forest clan"), it doesn't have to be this name I just picked it out of the guide book. The Na'ring feel they cant trust the Omaticaya as Jakesully was once a human. Tensions between the clans heighten. Several clans back the Omaticaya like the Ikran clan of the Eastern sea and the Direhorse clan of the plains. Since the Ikran and the horse clan fought with the Omaticaya and know that Jake helped in fighting the humans, they know that Jake deserves to be Olo'eyktan.
Im not certain of what the Na'ring's true motives can be but maybe they want to live at the Tree of Souls so they can be close to Eywa. (Their motives are up for discussion)
During this time Eywa has been weakened enough so that she can't bring peace between the clans.
So...Civil War! A few hundred clans battle it out on the plains of Pandora, well away from the forestation so they wont do damage to any of Eywa's plant and wildlife. There is a certain honour that all the clans respect in war. Unarmed Na'i are spared and civillains are treated kindly.
After the dust settles both the Omaticaya and the Na'ring settle their differences as now Jake has proved he will fight to protect his clan and is a true warrior.
This movie's ending will almost seem that the trilogy ends here, Eywa has recovered and peace has been restored. No, very suddenly, gunships break through the clouds, with transport shuttles like the Valkyrie trail closely behind. Either Neytiri or Jake or another key character (maybe the red-painted Ikran leader) gets abducted. The Na'vi are forced back and retreat into the forests. Jake/Neytiri soon find themselves in a lot more trouble.
To be continued...
Overall this movie is generally darker than the first. This is to set a sharp contrast with the third movie, which will generally be a lot happier in mood and atmosphere.
Final movie: PANDORA.
Again, very soon after the civil war. Many clans of the Na'vi have been weakened severely. Perfect time to strike right? That's right the humans return with a vengeance ready to take Pandora once and for all. Jake's/Neytiri's prime motivation is to free the abducted character that was taken in the sequel. This happens very early in the movie and there isn't a lot of time where the main characters are split up. The abductee is freed early on in the movie.
The humans chose a different location to set up base. The next largest unobtanium deposit is in the oceans, close the Ikran clan. This movie will show a lot of Pandora's oceans and sea creatures (many of which are unseen).
Im going to leave how the movie ends up for discussion as I don't have much solid ideas at the mo



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