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Anime and Manga
- The pilots in Martian Successor Nadesico all have visible implants in their arms that let them interface with ships and mechs. On Earth they're strictly military, but they're used for more mundane purposes on Mars - so when Martian civilian Akito is zapped to Earth during a Jovian attack, everyone assumes he's a deserter from the war.
- Outlaw Star has Melfina, an artificial human, as a helmsman.
- The Navigators of Dune arguably qualify, albeit without the usual biomechanical augmentation; they use Spice.
- Odrade has a cyborg pilot for her shuttle on her trip to Junction in Chapterhouse: Dune.
- The protagonist of Genome is a genetically and, to a lesser degree, cybernetically augmented starship pilot. In a subversion, though, almost every human in the story is similarly enhanced (except the "natural" navigator, and even that's a rarity, as the job requires one to plot a course in multiple dimensions).
- The Master Captain in Great Ship verse. While she still looks fairly human on the outside, she is far larger than a normal person to help disperse heat as her skin is jam packed with computers, AI assistants, and communication systems to interface with the Great Ship.
- Ship captains and pilots in The Night's Dawn Trilogy have extensive neural implants for controlling the ship and mapping out trajectories. Physically modified Cyborgs are primarily used as engineers and for patching up damage - some of them are so heavily modified that they don't even need space suits to survive in the vacuum, instead just needing a bottle of oxygen.
- Katherine Kerr's Polar City Blues has Lacey, a former (space) Navy pilot who has a neural-link port implanted in the back of her neck for connecting to ships, which has since sealed over.
- In the Revelation Space universe, the crews of interstellar spacecraft have formed their own culture, and most of them are cyborgs. A more extreme example is John Brannigan, a starship captain who became infected with a nanotechnological virus, causing his mind and body to merge with his ship in a very disturbing way. Even before the virus, he is described as being more robot than man, with the only visible trace of his humanity being his dreadlocks and the skin around his highly modified face.
- Vatta's War uses implants that allow access to certain funtionalities not normally allowed, as well as allowing mental activation and use of some controls.
- In the Vorkosigan Saga, starship pilots need special implants to interface with ship's navigation during wormhole travel. A recurring character is Arde Mayhew, who is unable to receive upgraded implants for medical reasons and so can't pilot more recent models of ship, and in The Warrior's Apprentice faces disaster with the decommissioning of the last remaining ship he is able to pilot.
Live Action TV
- Farscape. The living ship Talyn (who is himself a cyborg) forms a telepathic link with his captain by way of a cybernetic interface implanted at the base of the captain's neck. It's less for navigation than a instinctual need for a captain due to his native biology with a healthy dose of genetic engineering thrown in.
- Sandstrom the "augumented human" in Hyperdrive is a buggy prototype. It's not clear that her Unusual User Interface is actually any better than a normal helmsman would be.
- In spite of Star Trek's usual stance on cybernetics and transhumanism, Geordi LaForge wore a VISOR that connected to his brain and allowed him to see. In the first few seasons, his role on the ship was as the Helmsman, although he eventually graduated to Chief Engineer.
- And in Star Trek: Voyager, Seven of Nine uses Borg technology to create Voyager's Astrometrics lab, a 3D map of the space they're traveling through.
- The Navigators of Warhammer 40,000 are mutant helmsmen, capable of navigating through the Warp and allowing the Imperium to exist. Many officers in the Imperial Navy are so heavily augmented that they're often described as being more part of their ships than autonomous beings.
- Also, some ship captains, especially on Adeptus Mechanicus ships. One such captain appears in the first Gaunt's Ghosts book.
- Mechs in Rocket Age require a pilot with a neural interface to work correctly. The Nazis surgically add this to their pilots; the Ancient Martians may well have grown pilots with built in interfaces. The Europans also have technology that allows them to do the same; the only difference is that theirs is much less invasive.