My interpretation of the film's meaning

I just watched this for a second time, and decided that it was inspired by creation myths.

There's a god who creates things at the circus in the beginning. One of his creations floods the Earth, after which he picks it up and it becomes a mountainous desert. He cuts it in half, drops half, and plays with time trying to get the other half back. He tastes the primordial soup, and seems to decide that he prefers the planet whole. That entire sequence could be suggestive of wanting to start over again on many levels, especially because you can see disasters reversing themselves when he turns back time.

When the cats sail into the area full of machinery, it looks to be a representation of heaven, partly because the god had similar machinery and partly because the kitten finds the flower his sister needs there (a representation of finding her soul). They make their way back home and celebrate, but you see that the god is planning to eat the Earth whole, which explains the catastrophic ending.

So basically, on one layer it's about a hungry humanoid deity trying to eat the Earth (which could have an environmentalist meaning), and on another layer it's about a kitten traveling the world to save his sister from death at a particularly inconvenient time. The ending suggests the theme of futility, because the kitten goes to all that trouble and succeeds only to have the effort be pointless, which makes me think that the entire film could be a tribute to Nekojiru's suicide -- she created this world and these characters, only to be overtaken by a proverbial or literal sense of futility that caused her to kill herself, and so destroyed them.