Final Fantasy: The Spirits Within (2001) on Netflix

In the year 2065, a meteor has crashed onto Earth unleashing an invading race of millions of strange phantom-like alien creatures who roam the earth, decimating field and city alike, threatening to extinguish life itself. But when a brilliant young female scientist, Dr. Aki Ross makes a last stand on Earth with the help of a ragtag team of soldiers against an invasion of alien phantoms. She seeks information about their purpose and physiology, assisted by her mentor Dr. Sid and the Deep Eyes military squad of courageous Captain Gray Edwards Aki's old friend. Tension develops between Aki's quest to stop the alien onslaught through study and the more extreme solution favored by the vengeful, saber-rattling General Hein, who would destroy both the aliens and the Earth itself!