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Arpeggio of Blue Steel does this with actual naval ships, though the technology in said ships rivals that of most spaceships which would feature this trope. Interestingly, one of the human characters actually inquire about why all of the ships feature female avatars. The mental models state that humans have always referred to ships as "female", so logically they would be represented that way. See the Real Life entry for further details.
Kashimashi: Girl Meets Girl: the ship Jan-puu◊, who crashes into Hazumu, is the ditzy and affectionate type. She considers the crash that killed Hazumu and set the series in motion to be her first kiss.
Lost Universe has Canal Volfied◊, Meido-outfitted hologram with greenish-blueRapunzel Hair. Though she's well-aware of her nature as the ship's mind and can get very hyper when it comes to supplementing the ship's weaponry (which she refers to as "accessorising"), she's also got a very human-like personality. She has a particular distaste for Millie because Millie is insistent upon being the ship's cook... ignoring that she blows up the kitchen every single time.
Narue No Sekai: Bathyscaphe, Kanaka's ship and guardian, is a serious and matronly type...but she has her softer side.
There's another one called Haruna who is actually a deserter from the army who is hiding on earth. She's really nice, though.
In one instance Haruna gets overexcited and summons her ship form to welcome some visitors to the hotel she works at, much to the chagrin of everyone there.
Outlaw Star: Melfina, who seems at first to be a shy teenage girl, is soon revealed to be the living navigation system for a very advanced starship. The rest of the ship's functions, however, are controlled by Gilliam II, the ship's male computer system.
The space train, Galaxy Express 999 gets upgraded with a Spaceship Girl in the second series.
However, the trope is inverted with Captain Harlock's Arcadia. Tochiro, Harlock's buddy and the ship's builder, transfered his own consciousness into the spacecraft, making it male.
A variation of this was done in Vandread with the character of Bart. Though he just synchronizes with Nirvana, not becomes her.
GaoGaiGar's Penchinon is a subversion. After Pasdar is destroyed, it is revealed that he is the AI system for Soldat-J's J-Ark. All Penchinon really is...is an eye. Also subverted because, even in his 'old' form, Penchinon is some kind of... anchor-eyed, boat-person with a spinning head (but no neck), big teeth, a sailor uniform, and a tendency to go "BREEEEEEEEE!!".
At least two of the Vaia ships in Infinite Ryvius possess a "Sphix", a physical manifestation of the ship's control system. Unsurprisingly, the titular ship has the Spaceship Girl and in a slight twist, the "final boss" has a Spaceship Bishounen.
In Zone of the Enders Dolores, i, the eponymous Dolores has a ridiculously advanced AI making her a Humongous Mecha girl. She develops a crush on her pilot, and day-dreams of being in storybooks and a waitress, among other things. At the end of the series, when her body is destroyed, they transfer her AI to a ship. She complains that makes her feel fat, since her consciousness isn't stored on Metatron anymore.
Near the end of the first season of Full Metal Panic!, Kaname synchronizes with the Cool Boat, after which she's seen, naked, translucent, and making movements that the Tuatha de Danaan follows.
If Epileptic Trees are to be trusted (and ridiculously advanced AI is a qualifying trait for this trope, natch), Yukikaze from Sentou Yousei Yukikaze may be this. That is, minus the human avatar and all.
Stella Irvin of the Hückebein in Magical Record Lyrical Nanoha Force is another example of someone who can synchronize with her ship, to the point where she seems to be able to use her Healing Factor to repair damage on the ship while they're linked. This leads to disastrous consequences for her when the Hückebein's ship gets struck with the Zero Effect.
Kate Rose from Trinity Blood she is the basically the AI of the flying ship "The Iron maiden", although she's also a Wetware CPU whose body is comatose, she's been inside the ship for so long that she often refers to the parts of the ship as if they were her own appendages.
In One Piece, the Going Merry has a spiritual avatar known as a "Klabautermann" which, in dire circumstances, is capable of repairing the ship. Its gender is indeterminate.
In the CrossGen title Sigil, a female character remains a hologram tied to the ship's computer throughout the series.
In Runaways, when the group gets back together after the death of the Pride, Chase insists that the Leapfrog is a he, as there is enough estrogen on the team already, thank you very much.
In Power Pack, the kids argue over whether Friday is male or female.
The Marvel Comics character Star Lord has a sentient ship with a female persona. At least in the 1980s. Yep, the ship was in love with him. (She once generated a humanoid form to assist him when he was seriously injured.)
Wandering Star. The female alien Elli has the ability to physically merge with the Wandering Star's systems and run the ship in a far more efficient manner than when operated manually. She spends the majority of the series this way, within the ship, and communicates with the rest of the crew through the intercom.
In the Doctor Who comic miniseries "The Forgotten", in which the Doctor and Martha Jones find themselves in a museum devoted to the Doctor's past lives, Martha turns out to be a mental projection of the TARDIS itself, who can take on the form and personality of anyone who has ever traveled in the TARDIS, to aid him in a fight against an invader. Most of the personalities it takes on are female (but then, so have been most of the Doctor's companions). A similar idea would surface in the TV series later on.
In the Doctor Who Magazine strip "A Life of Matter and Death", the TARDIS manifests a mental projection of herself in the form of a veiled grey lady.
Moira, the Second Officer aboard the USS Crazy Horse, is an Artificial Intelligence who takes control of the ship's computer. Like other computers in Star Trek, she has a voice interface, but unlike them, she is also a woman, either in her organic simulacrum, or by projecting a hologram of herself.
SAL9000 in 2010 (played by Candice Bergen) is almost neuter, but female (and sounds very like Eldon Tyrell's computer in Blade Runner).
Inverted in Babylon 5: Legend of the Rangers, in which the weapons officer enters a holographic chamber in which she sees everything from the ship's own point of view, and fires weapons by throwing punches.
The Ship Who Searched by Mercedes Lackeyfeatured a brainship who financed the creation of a remote-operated android accessory so she could be her human partner's... partner.
Another book from that series has a brainship who had gone through a terrible traumatic event; in therapy a counselor had her channel her emotions and frustrations into art, and eventually had her create a self portrait. He expected her to paint a projection of herself as a human, if she hadn't had the genetic defects that landed her in a brainship, but she painted her shipself with some anthropomorphic elements.
In the Doctor WhoEighth Doctor Adventures novels, ultra-advanced TARDISes from the future could use their chameleon circuits to take human form. The one we meet appears as an attractive young woman (in an amusing Continuity Nod we're told she was once stuck as a 1960s policewoman). The Doctor's cyborg companion Compassion later takes on characteristics of the TARDIS and became the prototype for the class.
In the Big Finish short story "The Lying Old Witch In The Wardrobe" by Mark Michalowski, the TARDIS manifest a female avatar who kidnaps Romana out of jealousy shortly before "Destiny of the Daleks" and acompanies the Doctor throughout that adventure, including faking the regeneration scene at the start.
Xyon's ship is controlled by a female personality that was apparently a criminal before her death.
Later in the series, Robin Lefler's mother, Morgan becomes Excalibur's computer. Extra poetic because Morgan Primus is identical to all characters from the TV shows who were played by Majel Barrett Roddenberry. All Federation ships have a Computer Voice that is also done by Barrett.
Darcy in Vampirates "describes herself as "Figurehead by day, figure of fun by night!"
Another male example appears in the Revelation Space series, where a cyborg captain is melded with his ship by alien nanomachines. His consciousness is apparently distributed across the ship's systems, but he can still project an avatar of himself when it's useful.
Redemption Ark, the second book in the main trilogy also has a Spaceship Boy, though this time in the form of a sentient simulation of a criminal who was saved from termination by one character's father; the character in question is of course the one who owns the ship, and believes that she has an unusually helpful intelligent interface installed.
Inverted in the Iain M. Banks novel Matter; the Special Circumstances vessel 'liveware problem' has a man as its human avatar, and offers to sleep with one of the protagonists.
Ships and other structures run by Minds in The Culture series often have thousands of these (which doesn't even begin to test the computing power of a Culture Mind). Some of them are indistinguishable from other humans (this has caused at least one character minor embarrassment the morning after); others are more obviously nonhuman.
In Yellow Eyes by John Ringo and Tom Kratman, a US Navy cruiser, the USS ''Des Moines'' (CA-134), is converted to serve as a weapon platform for combating the aliens (it's a Sci-Fi novel, after all) and has a AID installed to control it. However the AI was left on while shipping to Earth, and developed more sentience (and some mental instability, due to sensory deprivation) by thinking the human equivalent of 5000+ years (in real terms a month or so, because AI think fast). the AI then proceeds to buy a cloning device on eBay (a Running Gag in the book is that you can find anything on eBay) and the clothing of a famous actress for DNA, and creates a living avatar for the ship. The AID's personality later merges with the "gestalt" of the original ship (basically a composite of the leftover traces of her crew's strong emotions, and in The Tuloriad she and several similar entities are rebuilt as starships using materials from the original ships because the non-AID portions of their "programming" make them resistant to several security flaws in the original AID design. Which proves to be of great benefit to humankind.
Joked about in the book The Hunt for Red October, when it stated that American ships are shes, Russian ships are hes, and the intelligence community calls them both its.
In Robin Hobb's The Liveship Traders series, there are sentient ships with animate figureheads. Some of them are males, though. They are mostly considered as persons, with one captain actually courting his female ship to the point that his sexual partner and the ship consider each other love rivals. Not played for laughs at all.
Some Bolos are quite female and feminine while being space-capable, with male service crews reacting appropriately. A gender inversion (masculine Bolo, a female crewmember's fixation) also occurs.
The starship MIKRU-JON in Perry Rhodan uses a holographic avatar of a petite, young human woman after Perry Rhodan becomes her new owner and pilot. Pilots often melded their minds with the ship to increase her navigational abilities, leaving an imprint of their personalities behind in the process. The selfaware ship's personality is an amalgamation of all her former pilots.
Live Action TV
Andromeda and the titular starship, with her holographic and robotic avatars: Rommie, the ship's AI given an android body. The ship's AI also looks like Rommie, though the two became separate characters to a degree. Most of the High Guard ships of her class seen in the series had female avatars (with the explanation being that humans and a number of other species prefer female avatars), though we have had several on-screen examples of male AIs, usually portrayed by someone who appeared on Stargate SG-1 or Hercules: The Legendary Journeys.
The only real difference between Rommie and the ship was that the android avatar experienced emotions. When Rommie is destroyed, Harper creates a new Android named Doyle from the leftover parts, who thus has the same access codes as Rommie. She and Andromeda get into a fight over who should control the ship, thus proving their completely separate identities.
And if you're wondering if there was ever an episode where a High Guard captain got Robosexual with his ship's android... Yep. (It wasn't Dylan.)
Holly, the AI interface aboard the Red Dwarf, starts off as male but undergoes a virtual-sex change (as part of an Nth Doctor shift) between the second and third series. She disappears after series five along with the ship itself, and the male Holly returns at the end of series seven (twofold! The ship is actually a nanite recreation of the ship and its crew from a time before the accident, so its Holly serves Captain Hollister and has no relationship with the Boys from the 'Dwarf. The version of Holly on the watch Lister found, on the other hand, knows them but is suffering from 'computer senility' and is a bit less useful than Holly of old.
In an episode of Star Trek: The Original Series, an "upgrade" to the Enterprise's computer causes it to start talking flirtatiously and calling the captain "Dear". Kirk said that the folks the repairs had been outsourced to thought the computer needed a personality, "so they gave it one." Star Trek: The Next Generation and Star Trek: Voyager both had female voices for the ships computer- logical, since they were voiced by Gene Roddenberry's wife. The ships were never completely sentient, with a possible exception in TNG "Emergence".
In the TOS episode "Elaan of Troyius" the women of the planet Elas have tears that make every man the tears touch fall madly in love with them. Kirk is infected, but okay by the end of the episode. Spock explains what happened: "The antidote to a woman of Elas, Doctor, is a starship. The Enterprise infected the captain long before the Dohlman did."
There was a similar episode where B'Elanna had to persuade a rogue Interplanetary Missile Girl that it was targeting a noncombatant world. It wasn't just any girl, either - she'd reprogrammed it herself, and given it her own voice (the old voice was a Cardassian male which annoyed her).
In Firefly, River says she has merged with Serenity. This is subverted when it turns out to have been a ploy to get the crew out of a rather dire situation.
Moya on Farscape is a Leviathan, one of a race of living ships. She even gives birth to a bouncing baby spaceship. Other Leviathans, of both genders, (with mixed-gender pilots, sometimes) also showed up.
Except Moya isn't an "avatar" of herself— if anything, Pilot should serve this role, since he generally is the channel through which the crew interacts with Moya. He's also about as far as you can get from a cute girl...
In one episode of the original 1978 Battlestar Galactica, Starbuck flew the Recon Viper, which had extra engine power but no weapons. It was fitted with C.O.R.A., an intelligent computer controller that not only talked in a feminine voice, but also acted like an overprotective girlfriend.
The Cylon ships in the Re-Imagined Series have Hybrids as their central computer hub. Hybrids take the form of women laying in a cloudy tub similar to a regenerating tub. Hybrids are not supposed to be sentient and generally their speech is a string of ship operations. Some models and humans believe that the Rebel Hybrid also spouts prophecy.
There was an episode of the Buck Rogers where Col. Deering had to deal with an onboard computer in a criminal's ship with a bitchy female personality, eventually Wilma dealt with the problem by physically tearing out the CPU.
In Doctor Who, the Doctor has always called the TARDIS "she" and insisted to companions that she is sentient; the new series in particular has gone full-tilt into Doctor/TARDIS RoboShipping.
The episode The Doctor's Wife all but confirms that the TARDIS is indeed sentient and female. (Guess who his "wife" is.) The 'soul' of the TARDIS in the body of a human gets to actually walk around (and it is as Crazy Awesome as you'd expect.)
Also, to keep himself focused when dying (exceedingly painfully) from poison, the Doctor has the TARDIS create a holographic interface, which is capable of looking like anyone. He finally settles on the child version of current companion Amy. However, she definitely doesn't act like Amy, speaking more like a standard Computer Voice (but giving one moment of Amy-ness as moral support.) Interestingly, a comic book miniseries involves the TARDIS manifesting holograms of companions, but it's... different. Read above in that section if you dare.
In a somewhat darker example, the Controller from "Bad Wolf." She's more of a Satellite Girl, but she controls all the data coming into and going out of the Gamestation. However, is (or was) human, and basically wired up to be part of the computer.
His girlfriend Ginn already beat him to this, along with Amanda Perry and Franklin.
On one episode of The Suite Life on Deck, Arwin makes an A.I. for the cruise ship that will control all the main processes of the ship. It becomes evil and eventually manifests itself as a Robot Girl, who falls in love with Cody.
In Silversun, Pancha is this, despite being born as a normal human and initially believing herself to be one. A mechanical implant in her brain gives her a telepathic connection to the ship's computer.
In the CBC radio comedy series Canadia 2056 the main computer of the ship, the Canadia, starts off having a female voice simply because he captain chooses it, while the French-Canadian Commander Margaux prefers the voice of a French-Canadian man. Latter in the series, the computer becomes sentient do to the interference of a Wish-Granting Sentient-Cloud being, and soon develops a crush on the captain, eventually leading to her crushing an American captain with a car, all because she thought he was trying to steal the captain from her. Actually, not very comedic sounding...
Serves as a Tomato Surprise in a vignette in the Transhuman Space book Deep Beyond, in which a girl the viewpoint characte meets in virtual reality, who is a crewmember on a USAF spaceship with a crush on the captain, turns out to actually be one of the ship's smart missiles.
Cortana in Halo: Combat Evolved, though the ship in question doesn't last as long as she does (although Master Chief's armor is apparently very similar to a spaceship, and the time she inhabits a Halo ring would probably count).
Karan Sjet from Homeworld. In truth, she is a scientist that sacrificed herself to become the Mothership's core, and is now the Mothership's voice and "soul" through the entire game. In the sequel she continues being the Mothership, but the ship itself changes.
All Bentusi are rather literally bound to their ships, therefore this becomes true of all the female Bentusi out there. You'd think there would be some, despite the ubiquitous male narrator.
The Cho Aniki Super Famicom Fighting Game features a literal spaceship girl as one of the playable characters, a flying steam-driven machine-girl, Mami,◊ with three little crewmen on her back who can be used as weapons.
Gadget Trial has been described as a fusion of turn based tactics games and mecha musume, and has the player control tank, artillery, and other girls who personify military hardware.
The 100-Series Observational Realians on the Durandal from XenoSaga.
Much like Dolores in the anime, A.D.A. in the main series and Parshti in Fist of Mars both undergo character development into this. In the second game, the new pilot of Jehuty actually teases A.D.A. about her apparent crush on her original pilot.
System Shock's Shodan is a spacestation girl. The sequel gives us Xerxes, a spaceship guy who eventually gets hacked and sublimated by a resurrected Shodan, allowing her to finally be a spaceship girl at last.
Averted in Albion, where the computer of the spaceship Toronto is represented by a masculine android "AI body" known as Ned. Later it turns out there's a whole bunch of armed Neds hidden on the ship in case anyone gets rebellious. At the very end, you see the core AI itself, a very decidedly neuter mechanical thing inside an indestructible black tin.
EDI, your new ship's AI from Mass Effect 2. No body or even image of one, but she's got the voice and personality. Her femininity is confirmed by both one of the engineers of the ship, who is afraid of the Estrogen Overload in the level, and by the ship's pilot, who sees the AI as a girlfriend/mother figure...eventually.
Now if only her holographic representation wasn't a ball-on-a-stick. This contrasts with all the various non-sentient "VI's" that often do have human(oid) holograms. This was done intentionally to prevent the crew from empathizing too much with a potentially dangerous AI.
In the Extended Cut of the Control Ending, after uploading her/himself, Shepard was recreated as an AI entity to replace the old Catalyst as the controller of the Reapers.
EVE Online gives us AURA, the universal AI that acts as the (feminine) voice for your ship. Or rather, every ship, regardless of who is flying it. It's a bit disconcerting to have any ship from a harmless shuttle to a fleet-destroying Titan talk to you in the same calm, female voice.
Post-Brain Uploading, Samus' former CO Adam in Metroid: Fusion is another spaceship guy, although it takes a little while for her to realise that it's actually him. Made a little awkward by the later revelation in Metroid: Other M that he was something of a father figure to her when he was alive; now she has a ship for a dad.
While we're on the subject of OtherM, we have MB, the Mother Brain Expy. She built an android body for herself, and she looks exactly like a normal human. She manages to fool both Samus and the player into thinking that she's Madeline Bergman, the head scientist.
Ace Online has the Akron First Fleet Flagship, which can be owned by the brigade of a certain nation after a war that takes place every 6 days. The main computer of the battleship manifests itself as a hologram of a seemingly female robotic head. The hologram itself doesn't interact with you apart from giving you management options for the base you own, though. Although one has to admit, according to the storyline, the Akron was built by Barkians, and Bark city was destroyed around 140 years prior to the player's timeline, which means that the poor hologram girl has been trapped alone for 140 years, maintaining an abandoned ship that gets some nasty wars between ANI and BCU every 6 days and then it has to cope with brigade members that are possibly not nice people over and over again. I would probably not enjoy it very much.
Indie game Analogue: A Hate Story introduces the archivist AI projection of a Generation Ship early on in the form of *Hyun-ae. Later, the protagonist gets to load up and meet *Mute, who puts a sexist spin on this trope.
Kantai Collection features personifications of WWII warships who otherwise fit this trope to a T. A somewhat strange case here, as while the girls ARE the ships, they can still equip the weapons and radar that they would be able to use as warships. Enemy ships also qualify, with the exception of the smallest destroyers.
The webcomic Krakow parodies this trope mercilessly with the "planegirl" story, starting here.
Schlock Mercenary's starships have embedded AIs that assist in the running and maintenance of the ship, that develop a hologram avatar that gives the meatbags inside the ship something to focus on when they're trying to talk. Most of these are actually male, probably to instill respect in a male-heavy military environment, but the Athens had Athena, a blue-skinned, red haired human girl. When the characters reunite with Petey and discover that his ears have become prodigious, he informs them that the algorithms determining an AI's hologram avatar are outside the AI's control, but the bigger ears indicate moving up in station, as it were. Incidentally, only two AIs aren't subject to this-Ennesby, an ex-computer virus and boy band with a separate robotic body, and TAG, the AI of the Touch-and-Go; this is because they both reside in physical units as opposed to the ship itself (although TAG does appear to have his rather firmly affixed to the floor of the computer room).
After his recent mental breakdown, TAG has had a personality reconstruction, courtesy of Ensign Ventura. In a re-inversion of the trope, he is now a she, and she has renamed herself Tagioalisi.
Sheila the tank (later transfered into various other vehicles and structures) from Red vs. Blue.
In the Bollywood Halo IGN April Fools parody Cortana is presented as a more literal and straight version of this trope as she is shown as a living human controlling the ship not a hologram. It is also implied in the parody that she has a (possibly) romantic relationship with Master Chief.
Starwalker (aka Starry) in Starwalker. She uses a holographic avatar of the woman she used to be. AI ships are common in the story but she's unusual in having a personality.
Nimue, the AI from Atop the Fourth Wall. She not only has the box in Linkara's apartment to communicate with him, but she also is Comicron 1's mind and ethical controls. We also see her have a "physical" body in her confrontation against Lord Vyce's pure data self during the most recent review of a 2001: A Space Odyssey comic.
Parodied in the Futurama episode "Love and Rocket", where upgrading the Planet Express ship's computer caused it to become a love-obsessed and unbalanced female voiced by Sigourney Weaver, no less! Interestingly, the voice was male by default, until they fiddled with the settings.
As mentioned in the introduction, the British, Americans, and other English-speaking nations have for hundreds of years referred to their ships as a "she." More to the point, during the Age of Sail it was not uncommon at all for sailors and captains to view their ships as living members of the crew, with distinct personalities—providing a historical foundation for this trope. Naval historians like Ian W. Toll have related accounts where captains would carry on conversations with their ships. One such captain was reputed to have said that "a ship can do everything but talk, and sometimes she can do even that."
The tradition of extending personification to aircraft is more visible with actual airships than it is airplanes—the United States Navy, for example, used to have two airships that acted as Airborne Aircraft Carriers, the USS Akron and Macon. Both were treated as if they were naval ships, right down to referring to them as female.
Other cultures have different traditions when it comes to giving ships a gender, if they do. Some consider ships male instead of female, while others have even more specific guidelines.
Among Russians, the rule is to "use the pronoun (adjective, past tense form) that is grammatically correct." Therefore, the ship's gender can vary according to what type of ship it's called. For example, the missile cruiser Moskva is considered male, but is female if referred to as a cruiser. The Oscar-class submersible cruiser Tomsk is male, but female if called a submarine. The research vessel Vityaz is male, but is neuter if referred to as a steamship.
Many commercial and military systems (such as GPS devices or collision/altitude alarms aboard aircraft) are female voiced—which will likely result in female avatars and AIs when technology reaches that point. It's not simply for aesthetic reasons, either: research by the United States Air Force has demonstrated that a female voice is easier to hear and understand under high stress situations (such as air combat).
Later research has been contradictory on this point, however—one study claims that a Creepy Monotone may have a better chance of recognition and understanding than a female voice.
Other research has claimed that female voices feel "safer" to listeners, but that this may be because HAL from 2001: A Space Odyssey has soured the general public on male voiced computers through Pop-Cultural Osmosis.
Concerning aircraft alarm systems, these are sometimes nicknamed "Bitching Betty" by pilots in North America (or "Barking Bob" if the system is male voiced).
The German Kriegsmarine averts this trope with the battleship Bismarck. Admiral Erich Raeder insisted the Bismarck be designated as a 'male' vessel at all times. Doesn't stop modern Germans from refering to that ship as a "she" every time it is mentioned.