Even if you really, really want to write the numerals instead of ten thousand (The Chicago Manual of Style says not to do that, but whatever floats your goat) the comma is in the wrong place. It should be 10,000.
In the second sentence, form should be from. Oddly enough, the double-zero is correct as numerals.
Ten thousand years in the future, Earth is one giant city, the lower levels long ago abandoned. One day, an elevator starts to ascend from level 00.
(It may be a little less awkward to change long ago abandoned to abandoned long ago, but the original version does put slight emphasis on the fact of the abandonment rather than on when it happened, so it may be better as it is, depending on what the author intends.)