Rise of the Planet of the Apes ends with James Franco and Caesar having one last emotional moment ("Caesar home," the ape croaks before disappearing into the trees with his buddies) but that wasn't always going to be the finale. That was a last minute addition, as the original ending had Franco's character dying.
At the hands of humans, no less. The original ending had Franco's character being shot to death by armed humans who have chased the apes into the forest. The ape horde descends on the people and tears them to pieces, a reversal of the opening scene where Bright Eyes is captured in the jungle. This isn't the only change from an early version of the script - originally
Rocket Koba and Caesar had a big brawl at the end as well. In fact lots of things changed lots of times over the course of the script's development.
Everybody hurried back to set this summer, just a month before release, to reshoot the ending. Considering the work required to animate those apes, that was a pretty big deal (and part of why I don't believe the final budget numbers on the movie).
It's unclear why Fox changed the ending, but apparently the original finale will be available on the home video release.