Nothing happens by coincidence in The Matrix - even the naming of a ship. Zion is a civilization caught between futurism and poverty. The last remaining dregs of humanity are always hungry and permanently fearing the Machine threat, but The Matrix takes place within a dystopian future centuries after full societal collapse, so the remnants of a technological renaissance still linger, giving Zion access to wildly advanced computers, DJ gear, and powerful hovercraft.
Zion's hovercraft fleet provides a rare thread between mankind's underground haven and the outside world. Soldiers like Morpheus and Niobe ride their ships through tunnels all the way to Earth's metallic surface, allowing them to rescue new recruits like Neo from the Machines' giant battery farms. Each hovercraft is also equipped with terminals for accessing the Matrix simulation. Whenever Keanu Reeves Neo, Carrie-Anne Moss' Trinity, or any other hero is shown kicking digital ass in the original Matrix trilogy, their real bodies are almost always located inside a nearby hovercraft broadcasting pirate signals into the simulated realm.
Whether it be the word "Neo" or a feline cameo, everything in the Wachowski sisters' Matrix world is steeped with symbolism or hidden meaning, and that even extends to the naming of Zion's hovercraft which, contrary to popular belief, doesn't just involve finding a word no one can spell. Here are the hidden meanings behind The Matrix's ship titles.
The Nebuchadnezzar
The Matrix's most recognizable ship - captained by Morpheus and featured heavily throughout the original movie trilogy until its untimely destruction - is the Nebuchadnezzar, taking its name from biblical conqueror, King Nebuchadnezzar II. This applies in-universe too, since Morpheus paraphrases Nebuchadnezzar in the aftermath of his ship's destruction - "I dreamed a dream... but now that dream is gone from me." Morpheus' quote may help us fathom the true meaning of his hovercraft's name.
In the Bible's Book of Daniel, King Nebuchadnezzar receives a dream from the Gods, but can't understand its meaning (some translations claim he couldn't even it). Nebuchadnezzar obsesses over finding his purpose within this mysterious vision, stopping at nothing to decode the divine secrets that elude him. When finally interpreted (by Daniel himself), the dream promises a kingdom of God soon to come. It's a story Morpheus himself should be all too familiar with, since Laurence Fishburne's The Matrix character is driven by a burning desire to find The One, holding faith that his purpose will ultimately lead to Zion's glory. Naming Morpheus' ship "The Nebuchadnezzar" may, therefore, symbolize the journey and motivations of its captain.
The Matrix's parallel between Morpheus and the biblical tale of King Nebuchadnezzar II is deepened by The Matrix Resurrections. When Daniel interprets the King's dream, he reveals the rise and fall of Babylon through the image of a statue, while elsewhere in the same book, Nebuchadnezzar is punished by God for his hubris. When Neo reunites with Niobe 60 years after his death in The Matrix Revolutions, she reveals how Zion fell due to Morpheus' pride, but in commemoration, Zion's hero has been immortalized as - you guessed it - a statue.
Another, darker facet to the inspiration behind Morpheus' hovercraft name can also be unearthed. Nebuchadnezzar is infamous for the Babylonian exile, whereby many thousands of Judaeans were taken captive on the King's order. Their faith survived until being liberated by Cyrus the Great, who finally allowed the exiles to return home. The Machines' subjugation of humanity in The Matrix may work as an allegory for this period of history, with the Matrix representing the captivity of Babylon, and Zion standing in for Judea. The use of Nebuchadnezzar as a name for a ship striving to free humanity, therefore, takes on a bitterly ironic hue.
The Logos
Before she was chewing out captains and swigging synthetic alcohol in Io, Jada Pinkett-Smith's Niobe captained the Logos in both The Matrix Reloaded and The Matrix Revolutions. The Logos' most significant contribution is carrying Neo and Trinity into Machine City for the Matrix trilogy's final act. With the Nebuchadnezzar destroyed by this point, Niobe breaks protocol by lending Neo her beloved vessel, letting Trinity fly the thing straight into enemy territory so that her boyfriend might negotiate a truce with Machine leader, Deus Ex Machina. Niobe's ship is destroyed as Trinity smashes the landing, but it's this fatal final mission that uncovers a hidden meaning behind The Matrix's Logos hovercraft name.
Logos broadly translates into Greek as "word," but Aristotle used the term to describe an "argument made from reason." When applied to Christianity, "logos" falls closer to "word of God," and both interpretations could be deemed relevant in Neo's case. The Matrix makes little attempt to hide how Keanu Reeves' character mirrors Jesus Christ - reborn after being betrayed, the savior of humanity, dying in a cross-shaped pose, etc. Neo making a pilgrimage into Machine territory and bargaining for peace on behalf of humanity is, as far as The Matrix is concerned, the word of God - the Christian logos. Neo's peace is achieved by pointing out how Smith has grown beyond the Machines' power, and only The One has a hope of stopping him - a perfectly reasonable argument that satisfies Aristotle's definition also. Neo's arrival on a ship called the Logos, therefore, represents the purpose of his mission.
The Mnemosyne
The most recent entry into The Matrix's hall of hovercraft is the Mnemosyne, captained by Jessica Henwick's Bugs in The Matrix Resurrections. The Mnemosyne plays a very similar role to Morpheus' Nebuchadnezzar, not only rescuing Neo from enslavement (again), but carrying him toward a final showdown against a programmable antagonist (again). The Mnemosyne's moniker derives from the Greek Goddess of memory which, of course, relates directly to Neo's revival and subsequent reentry into The Analyst's rebuilt Matrix.
The Matrix Resurrections plays on the fragility of memory, with Neo made to believe he's a video game designer called Thomas Anderson, and the events of the past three films were merely a storyline he created. Neo's memories make valiant attempts to resurface, but are suppressed by reprogramming, generous doses of blue pills, and The Analyst's therapy sessions. Nevertheless, Neo's memory proves too strong, subconsciously creating the Morpheus/Smith modal that leads to his freedom. The remainder of The Matrix Resurrections is a constant struggle against lost memories, not only for the recovering Neo, but also for Trinity, who doesn't regain her old self until the final act. Since the strength of their memories lead Neo and Trinity toward salvation in The Matrix Resurrections, it's only natural that the ship rescuing them be named Mnemosyne after the Goddess of memory.
Curiously, Bugs' Mnemosyne also continues a pattern started by the Nebuchadnezzar in 1999. Morpheus' hovercraft evoked dream-like imagery - the biblical dreamer king, Morpheus himself being named after the Greek God of dreams, etc. The Mnemosyne taking her cue from the Goddess of memory asks an all-important question sitting at the heart of Neo and Trinity's second stint trapped inside the Matrix: what's the difference between a dream and a memory?
Other Ship Name Meanings In The Matrix Movies
The Vigilant - Making a brief appearance in The Matrix Reloaded, the Vigilant aids the Nebuchadnezzar and Logos, but is destroyed by Sentinels. There appears to be little significance behind the hovercraft's name, with various naval ships throughout history adopting the same title. The Matrix's Vigilant does, at least, show how a centuries-old tradition from human history can still exist in futuristic, war-torn Zion.
The Icarus - Many will Icarus of "ill-advised flight near the sun" fame, and naming a hovercraft after a character famous for his inability to hover seems unwise. The Icarus' name may foreshadow its destruction in The Matrix Reloaded - similar to their namesake, the Icarus' crew perish after taking a risky mission alongside two other vessels.
The Novalis - Destroyed alongside the Icarus in The Matrix Reloaded, the Novalis likely nods to the 18th century German author of the same name, and subtly continues to depict Neo as a Christ-like figure. Novalis' most famous work, "Hymns of the Night," explored the relationship between God and Man via a representative between both worlds, such as Jesus. In The Matrix's mythology, Neo very much plays the role Novalis was so interested in.
The Vishnu - Drawing from Hinduism, the deity Vishnu is charged with preserving Earth, reincarnating during dark times to restore order. That works as a mission statement for Zion in general, but fits even better as a real-world allegory for The One, who reappears over and over to protect humanity from Machines.
The Ganesha - Although its name is only confirmed in The Matrix concept art, the Ganesha also takes inspiration from Hinduism. No obvious story parallels, but it's certainly interesting how Zion retains a multicultural element - even after humanity's destruction.
The Gnosis - Among the many vessels destroyed by Sentinels during the Matrix trilogy, the Gnosis serves as yet another indication of Neo's true nature. The hovercraft's name has roots in Gnosticism - a belief system that claims each person contains a divine spark within them. That idea can be easily applied to Neo, whose own "divine spark" makes him The One.
The Osiris - Mentioned in The Matrix Reloaded, the Osiris is destroyed off-screen, but not before Niobe receives their final message warning of a massive Machine assault on Zion. Since the voice of the Osiris is akin to a message from the dead in The Matrix, it's fitting that the ship itself is named after the Egyptian God of the afterlife.
The Brahma - One of the less prominent ships in the Matrix trilogy, Kali's Brahma is named after Brahma, the Creator from Hindu mythology.
The Caduceus - When Smith successfully traverses into the real world via Bane in The Matrix Reloaded, he materializes aboard the Caduceus - a ship named after Hermes' staff from Greek lore. As the messenger of the gods, Hermes' symbol is often used to denote a connection between two worlds. Rather than the divine and human, however, The Matrix's two planes of existence are the digital and real. "Caduceus" foreshadows how Smith uses Bane - one of the ship's crew - to cross from one world to the other.
The Mjolnir - Rather more famous now than it was in 1999 (courtesy of Chris Hemsworth), Captain Roland's Mjolnir is named after the hammer of Norse God, Thor. No need to overthink this one - Mjolnir is the biggest ship in Zion's fleet, and very much worthy of its name in The Matrix.