Fern Gully/WMG

Fern Gully is an evil entity bent on taking over the world, and Hexxus was created to stop it.
Fern Gully is a collective Hive Mind of super-intelligent trees that seeks to wipe out all humans and cover the Earth in itself, destroying all other kinds of ecosystems and species in the process. It is the only forest in the entire world that grows through fairy witchcraft. The fairies, the only beings that can speak to the trees, all blindly worship it as a god; and they use their magic to help it grow anywhere it wants to because Earth's diverse ecosystems, such as deserts, can't all support rainforests.

Hexxus was created by human shamans when Fern Gully began to spread too far as a way to keep it under control, much like Shiva, the Hindu god of destruction. Hexxus acts the way he does because he was once human, and his supposed evilness stems from his eccentric personality; and he simply loves his job. He is now a force of nature, keeping balance in the world, fated to be released from his tree prison every generation by humans chosen by destiny to quell Fern Gully's rampant growth.
 * This would explain why Hexxus is the second most likable character in the film after Batty (come on people, Robin Williams!).
 * Alternatively, the creation of Hexxus went horribly right and ended up damaging the normal ecosystems surrounding Ferngully.

Hexxus is Tim Curry.
Based on the above, Tim Curry is indeed a force of nature in our world as well.
 * I, for one, welcome our new greasy overlords.
 * Then does that mean Batty is Robin Williams?

Hexxus is vampiric.
A verse in "Toxic Love" goes "I see the world and all the creatures in it, I suck 'em dry and spit 'em out like spinach" This indicates Hexxus drains life force or something similar from animals and plants as well as pollution.

Hexxus is an demon of Nurgle from Warhammer 40000.
He's a living entity of corruption that feeds on pollution and destruction. Nurgle is about decay and entrophy as well as disease, and the worlds under his control tend to be polluted. Just because we haven't seen him try to convert anyone into worshippers doesn't mean that wasn't on the agenda after taking his revenge on his captors.

On that train of thought, Hexxus is the Spider/Pennywise/IT
Same voice and everything.

Hexxus is Xana
Well, they look very similar, only this one talks. And they are both bent on corruption/pollution.

Fern Gully is set in the future.
For starters, it's the "Last" rainforest. Second, it would explain how the fairies have never seen humans. Mount Warning is a site sacred to the Aborignal people, correct? Perhaps they died out generations ago, with only the oldest fairies (Magie & Crysta's father) having vague recollections of them.

Fern Gully is actually mental construct within Instrumentality.
All the fairies working together, that is the whole everyone turning into tang, Hexxus is the negative part of Shinji's psyche and is sealed away and Zack is the part of Shinji that rejects instrumentality and is able to return, Crysta is Rei (or Kwarou depending on your ship) Oh, and that Lizard that wants to eat him, that is Gendo.

It also explains why the biology, geography and social demographics are all off. The entire thing is based on the bits and pieces Shinji has picked when he was in class and not getting his ass handed to him by the Angels.

Zack hallucinated the whole thing
Druuuuuuuuuuuuuugs, maaaaan....

Zak knocked up Crysta, and pregnant fairy's are very powerful. that is the real reason she could kick Hexxus' arse
That "remember everything" was just a bit too personal for not to be true.

Hexxus is the vengeful spirit of the Tweed Volcano.
The ancestors of the ancestors of the ancestors of the fairies sealed it off, and it was only in (sort of) recent memory Hexxus escaped from the depths of the earth. Seeing as the Tweed Volcano is not ACTIVE, hence the need for a fuel source.

Years after his adventure in FernGully, Zak is kidnapped, brainwashed, and loses all his memories...
...leading him to take on a new identity as none other than Wester. Hey, it's Yasunori Matsumoto doing both, what did you expect?

Batty is not actually a fruit bat.
Fruit bats, as mentioned on the main page, do not have radars and should be larger than Batty seems to be. The reason why he refers to himself as a fruit bat is because, well... he's Batty. I.E., he's crazy in the coconut.
 * Alternatively he is a fruit bat that was blinded via other means (say, testing of experimental eye drops) who believes he used to have a radar for the same reasons as above.

Magi predicted Hexxus would be free by the humans.
Hence why she's training Crysta when the moment came. The "killing" of the trees is also killing her too, which is why she died.

Some of Zak's credit cards are from his old days.
Because one of them said he's 16, and in the actual movie, he must be in his twenties.