I remember watching this movie as a kid, so probably about 10-11 years ago, give or take, although I don’t doubt the movie is most likely older than that. it had the animation style of treasure planet and the like, however it was NOT Titan A.E.
I think it was set in space, because I remember there being things that weren’t human and things got pretty high tech. The scene I remember the most was at a city or a station of some kind that got attacked, and whatever antagonist army it was, I don’t quite remember what they looked like, I think they were lanky and blue, but again, NOT Titan A.E. Whenever the antagonists would shoot a victim, the victim would turn into this weird goop and go into these passages or tubes or something that ran along the wall and into something, but I don’t remember what happened after that. I remember the protagonist a little, he was young, but not a child, and he and I think a female friend, but I’m not sure, escaped on what I remember being giant space mantas or something. It was all pretty brightly colored as well, and I remember being in awe at how pretty everything was. I’ve tried to remember this for years but can’t remember for the life of me what it is.