It is difficult to define what animes are considered science fiction. Any anime with giant robots or non-magical powers could be considered a form of science fiction. Here is a list of anime that I consider to be the best in terms of more standard science fiction.
Ghost in Shell
Ghost in the Shell is a great example of speculative science fiction. Set in the not too distant future, Ghost in the Shell follows a group of Japanese anti-terrorist unit called Section 9. Ghost in the Shell has a Blade Runner quality about it, combining police and crime drama with futuristic technology, notably cybernetic enhancements. The show also deals with the nature of human consciousness and the potential for Artificial Intelligence. I recommend the film and the two anime series.
Another great combination of noir and science fiction, Cowboy Bebop follows the crew of the Bebop as they hunt down outlaws as bounty hunters or deal with demons from their past. The animation is beautiful and the show itself is highly entertaining. The characters are rich and well developed and the stories very well thought out. Cowboy Bebop also plays on the idea outer space as the Old West, something that any Firefly fan will love. The show also has one of the best opening songs ever.
Full Metal Panic!
Full Metal Panic! makes the list because it shows some of the most practical side of giant robots. Full Metal Panic! combines speculative science fiction with real world application. The robots in this series are very plainly portrayed as they would be used today, as very advanced tanks. Full Metal Panic! has a fascinating setting and a terrific set of characters and one of the most realistic portrayals of giant robots that I have ever seen.
Darker Than Black
While not hard sci-fi, Darker than Black is still a great science fiction anime. Darker Than Black is set in world where certain individuals known as Contractors have special powers are used by governments, criminal organizations, and intelligence organizations in covert operations. What I like about this series is what I liked about Full Metal Panic, it shows the application of fantastical technologies or abilities as they would be used in the world today. The fear that arises when someone in fiction exhibits power is governments or other individuals would try to take advantage of them. Well in Darker Than Black, that’s essentially what happens. Another great aspect is that it shows the literal price that these people have to pay for their powers.
Mobile Suit Gundam: 8th MS Team
Any mention of science fiction anime would be incomplete with mention of at least one Gundam series. As with other choices on the list, I picked 8th MS Team because it seemed more hard science fiction. The 8th MS Team is not about aces piloting ultra-advanced prototypes or super powered machines. It is about a team stuck deep in the trenches of war. Their mobile suits are held together by prayer and duct tape. 8th MS Team combines war stories, fantastic science fiction, and a romance on the battlefield. 8th MS Team remains one of my favorite animes because it shows that while the war is sometimes won by the big guys in super robots, it is still fought by the little guys in their regular robots.
By no means is this a comprehensive list of great sci-fi animes. There are plenty of other ones that I highly recommend. This list was focused on animes that showed the actual application of this fantastic technology and that are more down to earth in terms of their settings.
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