I'm trying to recall the name of an animated sci-fi cartoon I rented out of the public library during the late 1990s. I can only remember a couple of scenes/themes;
It involved aliens
The plot, I believe, revolved around searching for this one important guy, he was wearing a trench coat and brown hat in the style of Indiana Jones.
The main characters I can't narrow down but it did involve a little girl whom was the daughter to one of the characters
Towards the end of the film, the man they were searching for had an imposter that looked exactly like him, but was an alien in disguise. The two of them had a little fight where the real one was victorious and unveiled the alien imposter. The imposter then killed himself I believe with some sort of capsule, twitching on the ground. I don't remember why the alien was disguised as the missing person, but it might have been framing him for something.
After this scene there was something where a large flying creature came and snatched one of the characters away (another alien I think) and one of the other characters started shooting at the creature in a vain attempt to save the guy. The guy wasn't really trustworthy to begin with, as I can recall.
one of the main characters (who I believe is the father to the little girl) was a rather tall and built man with blonde hair. He might have had glasses on but my memory can't recall. (UPDATE: Did not have blonde hair, had black hair and was tall and thin).