I was watching the last season of Gintama where Kagura's parent;s meet on a post-apocalyptic desert planet, & it reminded me of a few things, an episode of Excel Saga, Fist of the North Star, & this anime I saw only once on Anime Network; a Comcast On Demand channel that's no longer available, somewhere between 2003 & 2008.
I believe it panned back & forth between two protagonists who were not with eachother, but I only remember the woman. I recall her being blonde & in red skimpy sci-fi outfit, possibly armor. She could fly & she moved very fast. She was mute & never spoke once during the entire movie. She could fly & move very fast, reminded me of Lum from Urusei Yatsura. The movie started with her coming to a planet & the movie ended with the planet being destroyed & everyone wiped out of existence.
Based on the description, it must be the 4-episode "Maps" OVA. Although the blonde woman do speaks, everything else seem to match up, with episode 3 ending with the destruction of a planet (see from 21:07 mark):