The characters inhabiting Zion, humanity's homebase against the machines.
Captain of the Logos, Niobe is Morpheus' ex-girlfriend who now is dating Commander Locke. Not a believer in Morpheus' prophecy, Niobe does, however, believe in Neo and lends him her ship in the third film to reach the Machine City. She is an Ace Pilot, driving the Hammer hovercraft to Zion whilst under attack from an army of Sentinels. Along with Ghost, she's one of the main characters of the video game Enter the Matrix.
- Ace Pilot: Almost everyone views piloting a mechanical pipe as impossible; not only has Niobe done so, she's done it twice. Once in her backstory, and once in the third film using someone else's ship.Roland: Holy Christ, I didn't know this ship could do that! [...] God damn, woman, you can drive!
- Action Girl: So action-y that she even stars in a Matrix video game!
- Badass Normal: An ace-pilot and can hold her own against Agents when necessary despite not being the one.
- The Captain: Runs the Logos.
- Cool Shades: A Matrix trademark.
- Sassy Black Woman: Very sassy, especially against Morpheus and Locke.
- Working with the Ex: Niobe gets on well with Morpheus and it's implied they become a couple again at the end of the third film.
Niobe's Number Two, Ghost is the best gunner in Zion. He was released from the Matrix on the same day as Trinity, and has unrequited feelings for her. Along with Niobe, he's one of the main characters of the video game Enter the Matrix.
- All Love Is Unrequited: Ghost's love for Trinity is unrequited due to the latter being in love with Neo.
- Badass Normal: Despite not being connected to the Prophecy, he's still talented enough to be the best gunner in Zion outside of the Matrix, and inside of the Matrix is one of the few to have ever killed an Agent. In Enter the Matrix he has survived encounters with the Merovingian's thugs and fought Seraph.
- Cool Shades: A Matrix trademark.
- The Gunslinger: He's known as the best gunner in Zion and he shoots like nobody's business in the Matrix.
- Like Brother and Sister: Ghost and Trinity see each other as siblings of sort since they were freed from the Matrix on the same day; despite his continued feelings for Trinity, Ghost noted that he felt free when he learned that Trinity would only ever see him as a brother.
- Number Two: To Niobe.
Commander Jason Locke
The head of Zion's defensive forces, Commander Locke is quite angry a lot of the time, but wants nothing more than to defend Zion from the Machines, no matter the cost. He's in a relationship with Niobe, expanding on his feud with Morpheus further.
- The Brigadier: He strongly disbelieves in Morpheus' belief in the Oracle's prophecy.
- Four-Star Badass: He didn't get to that rank by luck or schmoozing; he kicks some machine butt in the real world.
- General Ripper: He claims he would be willing to put a gun into the hands of everyone in Zion to take down the Machines. Considering what's in store for the humans if the Machines win, it's somewhat understandable why he has that attitude.
- Good Is Not Nice: He may be the commander of the human forces, but...
- Hot-Blooded: Given that his job is to keep people alive and he's failing, its understandable why he swears a lot.
- Jerk with a Heart of Gold: Despite having a humorless personality to the point that people call him "Deadbolt" behind his back, Locke genuinely wants to protect Zion. He just has no tolerance for Morpheus' ways and can't understand why the Council keeps supporting him.
- That's an Order!: Often uses this to get his commands understood.
- A Mech by Any Other Name: Mifune's army consists of armoured personnel unit machines.
- Battlecry: "KNUCKLE UP!" *the APUs all arm their cannons and assume a firing stance* "FOR ZION!!!" *everyone opens fire on the Sentinels*
- The Captain: Mifune leads the APU squadrons, while Locke oversees the overall defense operation.
- Character Death: He is killed during the Machine army's assault on Zion.
- Death of a Thousand Cuts: He ends up swamped by the swarm of Sentinels, and dies with his face sliced and diced.
- Number Two: To Captain Locke.
- Passing the Torch: To Kid to open Zion's doors for the Hammer to arrive.
- Rousing Speech: Gives one to his APU troops."All right! This is it! Now you all know me, so I'm gonna say this as simply as I can. If it's our time to die, it's our time. All I ask is, if we have to give these bastards our lives... we give 'em hell before we do!"
- Shouting Shooter: He shouts at the machines as he's shooting the swarm of them after they managed to overwhelm the defenses of Zion.
The Kid/Michael Karl Popper
A young redpill who was freed from the Matrix by Neo and of his own will. Now a Tagalong Kid, Kid deeply believes in Neo's ability to save mankind and is his biggest supporter. He Takes A Level In Badass in the third film to defend Zion.
- Canon Immigrant: From The Animatrix ("Kid's Story" short).
- Falling into the Cockpit: Takes over Captain Mifune's APU, despite having never successfully qualified in the sims, although Captain Mifune claimed that he never qualified in the sims either.
- Tagalong Kid: His wide-eyed enthusiasm when introduced and eagerness to fight for Neo's cause seemed tailor-made to let audiences know that he was so going to die later on, however...
- Took a Level in Badass: In the third film he takes up Captain Mifune's APU to cut open Zion's jammed bay doors so the Hammer could enter and light off her EMP, and he lives to tell about it.
A redpill who is possessed by Agent Smith in Reloaded. In the real world, the possessed Bane physically harms himself and seeks mankind's destruction. During the films, he uses an EMP to disable a small fleet of hovercraft, preventing Zion's EMP counterattack and allowing the five ships to be destroyed, then attacking Neo and Trinity aboard the Logos, blinding Neo. He (or at least the Smith code possessing him) is then decapitated by the blind man.
- Beard of Evil: Bane's goatee serves as this once he's overwritten.
- Character Death: He is killed when Neo decapitates him with a pipe.
- Demonic Possession: Smith overwrites Bane's Matrix-self and then takes over Bane in the real world through the broadcast connection.
- FaceHeel Turn: Not of his own choice.
- Famous Last Words:Real!Bane: Oh, God.
Smith!Bane: It's not over, Mister Anderson. It's not over.
- Fantastic Racism: Inhabiting a human body does nothing to reduce it; if anything, this Smith is even more determined to exterminate us."I admit, it is difficult to even think, encased in this rotting piece of meat. The stink of it filling every breath, a suffocating cloud you can't escape. Disgusting. Look at how pathetically fragile it is. Nothing this weak is meant to survive."
- Grand Theft Me: Has his mind overwritten by Smith.
- Kick the Dog: Does this to Neo and mankind throughout the films.
- Manipulative Bastard: Bane gains Smith's intelligence and deceit.
- Off with His Head!: Neo braining Bane with a pipe explodes "Smith"'s head from his perspective.
- Something Only They Would Say: It takes several "Mister Andersons" and an "I want what you want" for Neo to accept that, yes, Smith has somehow followed him into the human world.Neo: It can't be. It's impossible.
Smith: Not impossible. Inevitable.
Captain of the Mjölnir, Roland is a grouchy and cynical man who disbelieves in the One and Neo's ability to stop the war.
- Agent Scully: Much like Locke, he's skeptical about the prophecy and the One.
- Ascended Extra: In The Matrix Reloaded, he only appears in the opening and ending scenes. He becomes a supporting character in the third film.
- The Captain: He's the leader of the Mjölnir.
- The Cynic: He has absolutely no hope for Neo and his supposed ability to end the war.
- Grumpy Bear: Very cynical despite what everyone else thinks.
- Jerk with a Heart of Gold: He may be apathetic and rude to everyone, but he does cares for his crew.
- Verbal Tic: He has a tendency to say "Goddamn" a lot.
Zee's partner and marksman
- Bald of Awesome: Has a crewcut haircut
Link's wife, and Tank and Dozer's sister.
The medical officer aboard the Hammer.
- Character Death: Bane kills her before making his escape.
- The Medic: She's introduced monitoring Neo and Bane's vital signs while they're unconscious.
- The Reveal: Specifically, that Neo's vitals and brain functions are like someone who's jacked into the Matrix instead of simply unconscious or comatose, setting up Morpheus, Trinity, and Seraph's attempt to free him from the Merovingian.