Well, maybe not everything. As everyone here has already stated, that ending threw me for a loop. I hated having finally understood just what was going on throughout the whole movie, and then getting another curve ball at the very end with no explanation. Except for the obvious, that Burton set this up for a sequel.

There were several "throw-in" sort of gags, too, which worked out nicely in my opinion:

SPOILERS

1.When Leo grabs the gorilla soldier's boot, the gorilla's line was the same as Heston's when he was captured, only substituting "human" for "ape."

2. Heston, as Thade's father, states "Damn them, damn them all to hell," before he dies, referring to the humans. No need for explanation here.

3. The brand symbol looks like the Oberon spaceship (which looks like the Trade Federation battlecruiser from TPM).

4. I saw "Nova" in the credits, but wasn't sure which character she played.

5. The ruins of the Oberon coincidentally looked like the Statue of Liberty.

6. The final scene, although still confusing, is reminiscent to the beginning of the POTA movie where Zira & Cornelius emerge from the spaceship to be greeted by 20th century humans, only this time in reverse.

Again on the topic of the ending, remember the original movies? There were two ships: Taylor's & Brent's. Brent's was pretty well bashed up, but Taylor's was in good condition, only sunk at the bottom of a lake. Although not explicitly stated, Zira & Cornelius must have fished the ship out, launched it, got caught in the same time/space anomaly Taylor did, and was sent back in time. It is entirely possible Thade did the same thing.

[ July 30, 2001: Message edited by: Dukhat ]

You remember how they kept saying apes are afraid of water. It would of been cool if the humans built damns and when the apes came they would release it on them. I can imagine Thade saying, "Retreat, retreat." Actually and think he would keep going and drown.
Didn't Thade die.

[ July 30, 2001: Message edited by: Dr Phlox ]

Also , after leaving the POTA , Leo's ship went BACK in time.

Dukhat - I felt the same way , after Leo left the planet I thought i had everything tied up and was very impressed with the movie , but the ending just to quote you , threw me for a loop. Obviously its a set up for a sequel or four but it was very badly done.

Okay ... the Apes from Planet of the Apes found the other spaceship, got to Earth, and made sure the Apes became the dominant species instead of humans. Somehow, ape history evolved rather similar to human history, with ...

My only explanation is that somehow, PotA and Earth ARE the same. Thade - who wasn't dead, remember? - was, after Davidson's departure, able to rise to power again somehow. This wouldn't actually be too difficult, given most apes weren't at Calima to see the truth and would still see humans as animals. Then, Thade accomplished his goal, eradicating humanity as a species and using technology gleaned from the Oberon's databases.

Thus, Leo has essentially screwed up twice: first by forcing the Oberon to search for him and thus condemning it; second, by leaving PotA at a crucial time and not consolidating the changes he made there.

Of course, this theory isn't very sound. Navigational readings indicated PotA wasn't Earth. Why did his chronometer appear to go forward then back (and note it appeared to only go forward 600 years, whereas Ari refers to "thousands of years" of history), which isn't excatly likely anyway? And you're telling me there was enough fuel on Alpha Pod to land, then take off again (from an Earth-like gravity well at that), then fly all the way back from wherever the Oberonwas orbiting, to Earth (in a few minutes), and land there?

Did You catch that last line from Ari ? About How in a thousand years they will say a man came from the stars and saved the world and no one would believe it?

I was thinking Perhaps over time the story had become screwed up and twisted so that Thade was credited with bringing Humanity and Apes together...

Why do you cap odd, and seemingly random words? Perhaps, in a thousand years, people will. Today, however, we only capitalize nouns and the beginnings of sentences.