You know what's cooler than a Cool Ship? A cool organic ship. A ship that lives and grows and heals any space battle damage as you go.
These ships can run the gamut from being completely non-intelligent (generally comparable to plants) to having animal like instincts (the crew often serves more as handlers than as pilots, in this case) or being completely intelligent and self aware. The last type tends to be viewed as female and often has a Spaceship Girl for an avatar.
The exact nature of the ships ranges from being merely Cyborgs, to fully Organic Technology. How organic they actually look varies greatly. These types of ships tend to be grown more often than made in a shipyard. Sometimes they'll even go so far and have the ship be a Space Whale.
The great thing about both the organic/semi-organic living ships is that they're a very easy way to make your series seem ultra science-fictiony by encasing organic bodies in sleek metal shells. If you want to go for something more alien, then you can take the Organic Technology route and have corridors that look like great big arteries.
The idea of a living ship also opens up plenty of story opportunities, simultaneously funny and serious. Imagine a show where the biological ship catches a cold, runs a fever, and keeps sneezing its occupants into space.
Not to be confused with Setting as a Character where the ship is only treated as alive by the cast. Or Mechanical Life Forms which are living machines. If the ship is a machine except for a "brain", it's Wet Ware CPU. Can overlap with Sapient Ship, though a living ship isn't necessarially sapient and a sapient ship isn't necessarially biologically alive. If it's a Living Cool Airship, then it's probably also a Living Gasbag.
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Anime and Manga
Tenchi Muyo!: The Juraian spacecraft are powered by living, semi-sentient trees. The parent of them all is not only fully sentient, but a goddess - and the alter ego of one of the main characters. Also, Ryo-Ohki and Fuku, who are the cute mascot characters that transforms into a Living Ship.
Vandread: the Nirvana (or more accurately its power source, the Paksis) is alive, but communicates more through feelings rather than words.
At one point, the Nirvana does have to go poop, as one of the characters puts it
The spaceships in Outlanders are gigantic bio-engineered organisms.
The Flying Dutchman from Soul Eater is able to turn buildings and vehicles into living things, starting with the Ghost Ship Nidhogg (capable of devouring almost an entire village in a single bite) and then moving on to an entire factory.
Part 3 of Jojos Bizarre Adventure has the cast boarding a seemingly-abandoned freighter which suddenly comes to life and starts trying to kill them. Suspecting the involvement of a Stand, they eventually discover that the entire ship itself is a Stand, powerful enough to be visible even to non-Stand Users (when Stands are normally Invisible to Normals,) and which starts rotting and decaying after its Stand User is defeated
Bioship, the resurrected version of Biotron from Micronauts.
Legends of Zita The Spacegirl has Shippy, a small organic ship that Madrigal gives to Zita. Looking like a cross between a bug and a flower, Shippy can receive Zita's commands telepathically. Initially it can't fly on its own and has to be fitted with external engines, but in a later scene when Zita's in trouble outside and calling to it, it literally shrugs off its non-organic components and flies to the rescue.
The Authority's home base, The Carrier, counts, even down to being a Deadpan Snarker.
Epoch: act completely autonomously and seem to be so advanced that they can change shape, resurrect the dead, and change between matter and energy forms with ease. It is theorized that they may have started life on Earth, controlling its cycles of extinction and recovery.
In Shark Tale, the fish use whales like humans use buses or cars.
It's subtly implied in the novelization of Pacific Rim that the Jaegers may be becoming this due to the drift technology.
Raleigh heard stories of crews being surprised in the maintenance bays by Jaegers twitching and shifting even though their Conn-Pods were deactivated and empty. It was part of Ranger folklore that sometimes when you dreamed about your Jaeger, the Jaeger felt the dream and moved with you.
The Culture: Look to Windward: Behemothaurs, giant flying creatures which double as airships for the creatures living on their backs.
Xeelee Sequence: a race of spacegoing, whale-like starships called the Spline, who intentionally modified themselves to be able to survive in space.
Arguably the Xeelee themselves, though they are a very...exotic kind of life.
In the Uplift novel Heaven's Reach, many Jijoan colonists are taken to explore distant galaxies aboard a hydrogen-based Living Ship.
Star WarsExpanded Universe: a new group of aliens called the Yuuzhan Vong introduced in a five-year book saga, New Jedi Order. This race organically grows everything, from clothes to communication devices to sewage disposal systems to weapons. Organic spaceships were inevitable. There's also Zonama Sekot, a Genius Loci planet that combines organic matter and technology to create living ships. It's known as the Rogue Planet because it also did this to itself. The similarities are not coincidental.
The Night's Dawn Trilogy: there are both spaceships (Voidhawks and Blackhawks) and habitats (space stations that can be tens of kilometres long) that are alive and sentient, based on "bitek", a kind of organic technology.
West of Eden: the Yilané have a civilization built entirely on genetics and selective breeding, and use gigantic genetically modified icythyosaurs for trans-Atlantic shipping.
Wild Cards: the Takisians use and breed sentient (or semi-sentient) ships. Dr. Tachyon's ship - which he named "Baby" - regenerates its "ghost drive gland" over a period of years or decades, after he burned it out trying to go real fast.
Saga of the Exiles: The Tanu and Firvulag arrived from another galaxy via a starship that was a huge living organism which used its own psychic powers to travel via hyperspace.
Xenogenesis: the gene-trading, three-gendered aliens have spaceships that are more or less plants that can be communicated with. Their seeds are planted on planets where they gradually take over the entire surface before launching off as independent spaceships.
Hyperion Cantos: the Templar create living "Treeships", gargantuan trees fitted with star drives. The treeships are made inhabitable by force fields created by weird space creatures that may or may not be sentient themselves.
Genesis Quest and its sequel Second Genesis: had ships made from giant spacegoing trees which caught comets in their roots for water and nutrients, and used reflective outer leaves as solar sails.
Star Trek short story: about young Ben Sisko and a previous Dax, which involves a species that uses living ships, and the ship is controlled by the crew, biologically linked together, although most of the crew are separate beings. The story resolves around another species that has a 3rd gender that links the first two genders together, to be able to mate, and a member of that species and gender ends up taking the place of a member of the ship's crew, due to her mental linking powers and other political reasons.
The Lords of Creation: In the Courts of the Crimson Kings: the martians are masters of organic technology. Their landships and airships are both grown from living tissue, though they are not sentient. The landships have backup "engines" that are essentially a kind of land-based squid.
The Polity novels: Jain tech is an organic thing and can grow living ships.
In Tuf Voyaging, the biological warship Tuf 'inherits' as the last surviving member of a freelance salvage team is specifically NOT sentient, though it could have been made so; there is mention of other Earth warships with AI installed mutinying and/or fighting each other.
The Fall Of The Galaxy, the fleet of the Bargon Empire almost entirely consists of small biomechanical raider ships instead of the Standard Sci-Fi Fleet, which is used by the other major human powers (the Galaxy and the Seven Systems' Union). These ships have proven to be extremely effective at operating both on their own and in small groups to conduct raids into enemy territory and wreak havoc with supply lines and even destroy major targets before jumping to safety. Despite the fact that the ships are crewed, the demands of fast-paced ship-to-ship combat require split-second decisions that are best made by the biomechanical brains of the ships themselves. Normal raider ships with electronic brains have proven themselves vastly inferior to the melding of rapid computer calculations and biological unpredictability.
Leviathan: is basically the lovechild of an airship and a blue whale. The British Empire makes lots of these half-machine, half-organisms.
Discworld: Great A'Tuin himself (or possibly herself), the giant turtle with the Discworld on its back, where all the books are set. It even has a self defense system, based on actual turtles, where it spins around to avoid meteorites.
It's not a spaceship, but in The Last Continent, the God of Evolution creates a plant that grows galleons as fruit in order to get the wizards off his island. It has a leaf sail, a trumpet-like flower that detects land in the crows nest, and the seeds are surfboards.
The Godwhale: the Roqual Maru is an organic plankton-harvester ship that was built on/in/around (take your pick) a blue whale.
Beloved in Walter Jon Williams's Angel Station is a member of a race of living ships, who use genetically-engineered servants to maintain them and do various tasks like load cargo, the most prominent of which is General Volitional Twelve, who is sent to study humans and act as her envoy. At the end of the novel, Beloved's trade (high quality drugs for computers) with the newly-discovered human siblings Ubu Roy and Beautiful Maria results in prosperity for both sides, although it is hinted that Beloved's "people's" exposure to humans will eventually lead to their demise.
Beloved is fully-organic, with parts grown instead of built. This still requires acquiring the proper genetic codes from other ships of her species. It is shown, however, that their navigational organs are horribly imprecise at jump calculations. When Ubu Roy offers simple mining computers for this purpose, they are significantly better at this.
Of course, these "simple" mining computers are light-years ahead of current computer technology, as they're able to process data at FTL speeds thanks to something called macro-molecules.
The Willflower from Colony becomes one of these thanks to engineereal evolution. Of course, this causes no end of problems for the crew until the end of the book when Eddie gets to meet the ship.
The short story the specialist is about several aliens species who make up a living ship, but this one has lost a certain part...
Boojum by Elizabeth Bear and Sarah Monette has Space Pirates using a boojum (a gas giant swimmer which has evolved into a spacefaring creature) to hunt down and eat metal-hulled spaceships.
Live Action Television
Doctor Who: The TARDIS appears to be technological, but at least some of it is "grown". And it certainly has sentience, though it cannot speak and only occasionally directly affects a story of its own volition.
Until "The Doctor's Wife", where the soul of the TARDIS gets put into a woman, and we get to hear her describe her adventures with the Doctor from her own point of view.
Eventually Expanded Universe managed to produce the humanoid TARDIS es, Type-103 or 104 in comparison to the Doctor's Type-40. Those were, indeed, capable of interacting with others normally with nobody the wiser. Eventually, a companion of the Eighth Doctor was transformed into this type of ship, and was used in this capability.
Lexx: the titular ship is mostly (and often gruesomely) biological. It can speak directly to its crew, and its hobbies include blowing up planets. Strangely enough, it even reproduces at the end of the series, spawning a smaller light-white version of itself when it dies...of old age. Since Little Lexx has no mechanical parts added to the hull or machinery of any kind like the original's cryo-pods and moth breeder bay, it's likely that the non-organic elements were added to the original as it was growing. Little Lexx even has a glowing angler horn.
Farscape: the Leviathans are living biological ships, who communicate through their permanently-bonded Pilots and were created by Sufficiently Advanced Aliens known only as the Builders to work for peace in the universe. One, Moya, is the main setting of the series, but various others appear in the show, most significantly Moya's son Talyn, who was created as a battleship through the interference of a fascist culture who once enslaved Moya and is unfortunately Ax-Crazy as a result.
Both the Vorlons and the Shadows use ships which are alive to some extent. Shadow ships are symbiotic and require a specifically prepared and hardwired pilot to merge with them. Vorlon ships are at least semi-sentient - they can sing, they're customized to be loyal to their captain, and they grieve over his death and would fall into rage if he was attacked. Both kinds of ships can regenerate and the Vorlon ship is shown to protrude appendages from its surface.
Several other ships seemed to have biological properties: the Soul Hunter ships, and the Berserker Probe both looked very similar to Vorlon ships. There were also some subversions: the Minbari built their ships to look organic but didn't actually have biotech spacecraft until the alliance with the Vorlons produced the hybrid mechanical-biological Whitestars. Minbari always had advanced crystal tech, but that's a different setof tropes. The Streib (who were only featured in one episode, where they brutally abducted Captain Sheridan, were also stated by JMS to lack biotech spacecraft and like the Minbari superficially mimic its appearance with their mechanical technology.
In the Expanded Universe trilogy The Passing of the Techno-Mages, the techno-mage ships are also said to be partially alive when "associated" (i.e. connected) with their pilots. This is due to a part of the techno-mage's chrysalis they used to train being integrated into the ship. The chrysalises and the implants are products of Shadow technology.
Battlestar Galactica: The Cylons of the reimagined series, despite their mechanical natures, use biotechnology in virtually all of their spacecraft; fightercraft-sized Raiders are autonomous biomechanical constructs (likened in dialog to trained attack dogs), while the larger basestars are at least partly organic and are controlled by a humanoid cyborg.
On one occasion, Starbuck experimentally cuts a hole into a crashed Raider's hull... only to find an almost completely fleshy interior. She manages to commandeer it by cutting out the Raider's dead brain and squeezing certain nerve chords to give commands to the mechanical parts.
Frak me... you're alive?!
By the end of the series, Galactica itself becomes one of these. When Boomer blows out a huge section of the hull due to an ill-timed jump, the rogue Cylons volunteer some of their biotechnological material to patch the empty spaces. At the same time, a brain-damaged Anders is set up as the ship's Hybrid.
Also, in the very first episode "Encounter at Farpoint", Farpoint Station is eventually discovered to actually be a living space-jellyfish-type organism that was forced to assume the form of a space station.
Stargate Atlantis: The ships used by the Wraith are organic and are suspected to be grown rather than manufactured. This is confirmed in a later season when Dr Keller is infected with a virus and begins to grow into a Wraith hive ship. Despite their organic nature they seem to possess little to no intelligence.
The series finale reveals that the only limitation to the growth of a Wraith ship is the amount of available power. When an Ancient ZPM module is plugged into a Wraith hiveship (already one of the largest ships in the universe), it grows to enormous proportions, thickens its hull to rival Ori shields (weapons that cut through Ori shields like butter barely dent the abnormally thick super-Hive armor) and grows larger-caliber energy weapons, turning it into the most powerful ship in the known universe.
The titular ship/submarine from SeaQuest DSV was partially organic. One episode even dealt with a biological infection of its hull/skin.
In Space Cases, the Christa is alive. This denies the cast a hyperspace shortcut back home in one episode. The gate controller refuses to allow them entry since Christa wouldn't be able to survive the trip through the gate.
Warhammer 40,000: The Tyranids are a completely biological race. Everything is some kind of animal, including huge living space ships.
The Eldar starships may also qualify. They're made out of wraithbone (a psychoplastic material solidified from pure Warp energy) instead of actual biological matter like the Tyranids, but wraithbone can heal from injuries and seems to be alive in some sense. The ships also possess a smaller scale version of the infinity circuit of the Eldar Craftworlds, giving them a limited consciousness (but no true sentience), and allowing the steersmen to control them as extensions of their own bodies. In some cases the ships may even be "crewed" by souls of dead Eldar placed into the infinity circuit.
Traveller 2300: The Pentapods have living starships which they engineered for —and from— their own species thousands of years ago.
Mage: The Ascension: The Progenitor faction of the Technocracy built a living spaceship called the Vivo. Many of them find it hilarious to refer to going somewhere in vivo. If you get this joke, you've spent too long in a lab.
GURPS: Spaceships includes this in divergent technology paths. If you have a powerful mage there are rules of zombifying your Living Ship.
GURPS Supers supplement Wild Cards. The 'Ishb'kaukab are a race of whale-sized, telepathic, sentient creatures that live in deep space. They have been tamed and genetically engineered by the Takisians into self-repairing spaceships.
The Reapers are finally revealed to be this: entire civilizations distilled into biological goo (while supposedly retaining consciousness somehow) which forms the core part of a massive artificial body.
The Leviathan of Dis, described as a "biological ship" found by the salarians, and apparently stolen by the batarians, was revealed to be yet another Reaper. Not necessarily obvious considering the Reapers appear to be entirely mechanical on the outside AND the inside; only thorough investigation can reveal that they contain a significant amount of living matter.
In Galactic Civilizations 2: Dread Lords, the Arnor and the eponymous Dread Lords both appear to use insect-like biological ships. The Iconians as of the Twilight of the Arnor expansion can also use Organic Technology augmentation to toughen their ships, and any Good-aligned civ can get access to a small amount of Arnorian battle armor, but their ships are still almost entirely non-living.
Prey: The world ship is part technology, part living tissue, with something that used to be human(probably) as the brain.
UFO Aftermath: The alien ships are revealed at some point of the game to be living things.
Starcraft:The Zerg have several units capable of traveling through space, including Overlords which can carry land units with them. The Expanded Universe adds the Behemoths, originally a race of Space Whales that were assimilated in order for the Swarms to leave their original homeworld Zerus. There's also the Leviathan a massive hulking Zerg that dwarfs the Terran Battlecruiser and it serves as Kerrigans Battlestar.
Creatures 3 and Docking Station: The Shee Ark and Capillata are grown in vats. Capillata even has some kind of brain/heart thing visible in the Hub section. They aren't shown to be able to communicate, but appear to be capable of running themselves.
The Beast of Homeworld: Cataclysm takes this trope and runs with it. Each infected vessel is its own "self", alive and aware. Add in a command ship, and all of the individual "selves" are assimilated into the whole, essentially becoming a living fleet.
Space Pirates and Zombies plays this trope mostly straight- if Zombie Critters kill all the crew of any ship- be it enemy, ally, or YOUR VERY OWN, the ship transforms into a purple-tinted dumb-but powerful monster ship which has partially organic hulls. Oh, and they regenerate hull HP. This trope is played even more straight with the Zombie Breeders- they are mostly organic , save for the random bits of spaceship in and on them. Because they generate Rez, they can replicate human ships without need of victims- this is why they can LAY EGGS which HATCH INTO FULL-SIZED BREEDERS.
In EV Nova, the Polaris grow their ships around artificial skeletons. The smartest class of ship have roughly the same level of intelligence as a smart dog.