Kinda cheating to call the Spirits Within a video game movie. It was titled Final Fantasy but was a wholly unique story and new characters and everything.
For another example, see Final Fantasy: Advent Children which is a sequel to Final Fantasy 7. It's pretty enjoyable.
And to be fair, most films based on other media don't directly translate their source material either. Oh sure, novel based films do, but most comic book movies seem to have plots written specifically for the movie, with elements from various comic issues mixed in. And most based on TV series usually have new stories too.