The human city of Zion defends itself against the massive invasion of the machines as Neo fights to end the war at another front while also opposing the rogue Agent Smith.

Agent Smith: Why, Mr. Anderson? Why, why? Why do you do it? Why, why get up? Why keep fighting? Do you believe you're fighting... for something? For more than your survival? Can you tell me what it is? Do you even know? Is it freedom? Or truth? Perhaps peace? Could it be for love? Illusions, Mr. Anderson. Vagaries of perception. Temporary constructs of a feeble human intellect trying desperately to justify an existence that is without meaning or purpose. And all of them as artificial as the Matrix itself, although... only a human mind could invent something as insipid as love. You must be able to see it, Mr. Anderson. You must know it by now. You can't win. It's pointless to keep fighting. Why, Mr. Anderson? Why? Why do you persist?
Neo: Because I choose to.
The Oracle: What about the others?
The Architect: ...What others?
The Oracle: The ones that want out.
The Architect: Obviously they will be freed.
The Oracle: I have your word?
The Architect: What do you think I am? Human?
Neo: I just have never...
Rama-Kandra: ...heard a program speak of love?
Neo: It's a... human emotion.
Rama-Kandra: No, it is a word. What matters is the connection the word implies. I see that you are in love. Can you tell me what you would give to hold on to that connection?
Neo: Anything.
Rama-Kandra: Then perhaps the reason you're here is not so different from the reason I'm here.
Trinity: Six hours ago, I was ready to give my life for you. Do you know what has changed in the last six hours?
Neo: No.
Trinity: Nothing.
Oracle: The great and powerful Oracle. We meet at last. I suppose you've been expecting me, right? The all-knowing Oracle is never surprised. How can she be, she knows everything. But If that's true, then why is she here? If she knew I was coming, why didn't she leave?
[sweeps plate of cookies off table]
Agent Smith: Maybe you knew I was going to do that, maybe you didn't. If you did, that means you baked those cookies and set that plate right there deliberately, purposefully. Which means you're sitting there also deliberately, purposefully.
Oracle: What did you do with Sati?
Agent Smith/Sati: Cookies need love like everything does.
Oracle: You are a bastard, you know that?
Agent Smith/Seraph: You would know, Mom.
Agent Smith: Wait. I've seen this. I stand here, right here, and I'm supposed to say something. I say, "Everything that has a beginning has an end, Neo."
[pause]
Agent Smith: What? What did I just say?
Trinity: I don't have time for this shit.
[fight ensues and she puts a gun to the Merovingian's head]
Trinity: You wanna make a deal? How about this? You give me Neo or we all die, right here, right now.
Merovingian: Interesting deal. You are really ready to die for this man?
Trinity: [cocks gun] Believe it.
Persephone: She'll do it. If she has to, she'll kill every one of us. She's in love.
Merovingian: It is remarkable how similar the pattern of love is to the pattern of insanity.
Trinity: Time's up. What's it gonna be, Merv?
Trinity: I wish I hadn't. That was my last thought. I wished I had one more chance, to say what really mattered, to say how much I loved you, how grateful I was for every moment I was with you. But by the time
[I knew I'd]
Trinity: said what I wanted to, it was too late. But you brought me back. You gave me my wish. One more chance to say what I really wanted to say... Kiss me, once more. Kiss me.
Deus Ex Machina: And if you fail?
Neo: I won't.
[as the machine drones swarm around him]
Neo: I only ask to say what I've come here to say. After that, do what you want and I won't try to stop you.
[the drones withdraw and resolve into a face]
Deus Ex Machina: Speak.
Neo: The program Smith has grown beyond your control. Soon he will spread through this city, as he spread through the matrix. You cannot stop him. But I can.
Deus Ex Machina: [shouting] WE DON'T NEED YOU! WE NEED NOTHING!
[the drones swarm around Neo again]
Neo: If that's true, then I've made a mistake, and you should kill me now.
[the drones swarm... and draw back into the face again]
Deus Ex Machina: What do you want?
Neo: Peace.
Mifune: 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!
The Architect: You played a very dangerous game.
The Oracle: Change always is.
Neo: It's been an honor, sir.
Morpheus: No. The honor is still mine.
Agent Smith: Mr. Anderson. Welcome back, we missed you.
[Agent Smith pauses and looks around at the multitude of clones he has created]
Agent Smith: Like what I've done with the place?
Neo: It ends tonight.
Agent Smith: I know it does, I've seen it. That's why the rest of me is just going to enjoy the show because we already know that I'm the one that beats you.
Mifune: [dying] They're coming... they're coming... the Hammer.
Kid: What?
Mifune: You have to open that gate. Cut the counter-weights. You can do it. Hurry, there's no time.
Kid: Captain, I... I didn't finish the training program.
Mifune: [smiles] Neither did I.
[dies]
Agent Smith: Get away from me!
Neo: What are you afraid of?
Agent Smith: It's a trick.
Neo: You were right Smith. You're always right. It was inevitable.
Rama-Kandra: That is our karma.
Neo: You believe in karma?
Rama-Kandra: Karma's a word. Like "love". A way of saying 'what I am here to do.' I do not resent my karma - I'm grateful for it. Grateful for my wonderful wife, for my beautiful daughter. They are gifts. And so I do what I must do to honour them.
Q-Ball Gang Member #1: The only way you're getting through this door is over my big dead ass.
Seraph: So be it.
The Oracle: Everything that has a beginning has an end. I see the end coming, I see the darkness spreading. I see death.
Mifune: How old are you, kid?
Kid: Eighteen.
Mifune: Should have said sixteen, I might have believed that.
Kid: All right, I'm sixteen.
Mifune: The minimum age for the Corp's eighteen. Sixteen's too young.
Kid: The machines don't care how old I am. They'll kill me just the same.
Mifune: ...Ain't that the goddamn truth.
Kid: Please, Captain Mifune, give me a chance. I won't let you down.
Mifune: You do, and you're gonna find that me and the machines got something in common.
Agent Smith: Can you feel it Mr. Anderson? Closing in on you? Oh I can, I really should thank you after all. It was, after all, it was your life that taught me the purpose of all life. The purpose of life is to end.
[after Neo ends up back at the same subway stop after running down the track]
Neo: Shit.
Roland: This is asinine. If you want to kill yourself, go ahead, but do it without wasting one of our ships.
Neo: You have to believe me. I have to go.
Roland: Bullshit. I'm captain of this ship, *I'll* say where it has to go. And believe me, this ship will go to hell long before I let you take it anywhere!
Niobe: He can have mine.
Roland: Niobe! You can't do that!
Niobe: Don't you even begin to tell me what I can and can't do with my ship after that little speech.
Morpheus: You've never believed in The One.
Niobe: I still don't.
Morpheus: Then why are you doing this?
Niobe: [re: Neo] I believe in him.
[to Bane/Smith, after he is blinded]
Neo: I can see you.
Ghost: Well it's nice to have something to look forward to.
Niobe: Indeed it is.
[after the machines stop attacking, at Zion]
Niobe: What are they doing?
[seeing Morpheus put his gun down]
Niobe: What are *you* doing?
Lock: Three captains, one ship. I assume the other two were lost under equally pointless circumstances?
Niobe: It's good to see you, too, Jason.
Lock: The council awaits your report. You'll forgive me for not attending, but I need to find a way to salvage this debacle.
Roland: Did I miss something here, Commander? I thought we just saved the dock.
Lock: That's the problem with you people. You can't think more than five minutes in front of your faces. That EMP knocked out every piece of hardware, and every APU. If I were the machines, I'd send every sentinel I had over here right now. "Saved the dock" Captain?, you just handed it to them on a silver platter!
Neo: What do you want?
Bane: I want what you want... Yes. That's it, Mr. Anderson. Look past the flesh. Look through the soft gelatin of these dull cow eyes and see your enemy!
Neo: ...No.
Bane: Oh yes, Mr. Anderson.
Neo: It can't be...
Bane: There's nowhere I can't go. There's nowhere I won't find you.
Neo: It's impossible...!
Bane: Not impossible. Inevitable. Goodbye, Mr. Anderson.
Neo: One way or another, I'm getting on this train.
Trainman: You don't get it. I built this place. Down here I make the rules. Down here *I* make the threats.
[the Trainman punches Neo, sending him flying back into the wall]
Trainman: Down here... I'm God.
Niobe: Neo...
Morpheus: He fights for us...
[Bane is pointing a laser gun at Neo]
Bane: Somehow familiar, isn't it? We've been here before, you and I. Do you remember? I do. I think of nothing else.
Neo: Who are you?
Bane: Still don't recognize me? 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. How pathetically fragile it is. Nothing this weak is meant to survive.
Deus Ex Machina: It is done.
Roland: Slow down! This ain't the Logos!
Niobe: Hold on to your lunch, Roland. Here we go.
[Niobe does a flip with the Hammer]
Roland: Holy Christ, I didn't know this ship could do that.
Morpheus: You saw the Oracle? What did she tell you?
Niobe: Same thing she always does: exactly what I needed to hear.
Niobe: Ah shit, she's got a fat ass.
[Bane has burned Neo's eyes out]
Neo: I'm all right, Trin... but I think you're gonna have to drive.
Trinity: If you tell me we'll make it I'll believe you.
Neo: We'll make it. We have to.
[about Neo]
Morpheus: I don't know what he can do to save us. But I do know that as long as there is a single breath left in his body he will not give up and neither can we.
[last lines]
Seraph: Did you always know?
The Oracle: Oh, no. No, I didn't. But I believed... I believed.
Sati: [frightened] He's following us...
Agent Smith: [opens door] Well, well, it's been a long time.
[to Seraph]
Agent Smith: I remember chasing you is like chasing a ghost.
Seraph: I have beaten you before.
Agent Smith: Yes, but as you can see, things are a little different now.
[Smith clones begin to file in. The Smith who has been speaking squats down in front of Sati and speaks to her]
Agent Smith: And you must be the last Exile.
Sati: The Oracle told me about you.
Agent Smith: Oh, really?
[chuckles]
Agent Smith: What did she say about me?
Sati: That you are a bad man.
Agent Smith: Oh, I'm not so bad... once you get to know me...
[more Smiths file in]
Bane: There is nowhere I can't go, there is nowhere I won't find you.
[about to break into a night club]
Seraph: There are no weapons allowed in this club. At the bottom of this elevator there is a coat check girl and, if we are lucky, a man to check weapons.
Trinity: And if we are unlucky?
Seraph: Then there will be many men.
Cas: I know how you feel, Zee, but you can't do this.
Zee: I have to.
Cas: Why?
Zee: [looking up from her bowl] Because I love him. I love him the same as loves me. And if I were out there and he were here, I know what he'd do.
Cas: [grabs Zee's hands] But you're gonna get yourself killed. It's crazy, Zee.
Zee: Maybe it is. But ask yourself, if it were Dozer, and you knew the only chance you had to see him again was to hold the dock, what would you do?
Cas: [pauses] Make shells.
[releases Zee's hands]
The Oracle: [referring to the Architect] Oh please! You and I may not be able to see past our own choices, but that man can't see past any choice!
[Bane/Smith has burned Neo's eyes out]
Bane: I wish you could see yourself Mr. Anderson... Blind messiah. You're a symbol for your kind, Mr. Anderson.
Morpheus: After everything that's happened, how can you expect me to believe you?
The Oracle: I don't expect you to do anything. I expect what I've always expected, for you to make up your own damn mind. Believe me or don't.
Agent Smith: This is my world! My world!
Morpheus: You're a hell of a pilot.
Niobe: Some things in this world never change.
Morpheus: But some things do?
Niobe: [sighs] Luckily... some things do.
Bane: Ah, Mr. Anderson, I see you are as predictable in this world as you are in the other.
Neo: What?
Trinity: He's out of his mind.
Bane: It may appear that way to you, but Mr. Anderson and I know that appearances can be deceiving.
The Oracle: [smells freshly-baked cookies] Mmm, I love that smell. I sure am going to miss it.
Agent Smith: [as he and his clones are about to explode] Oh, no no no no... no, it's not fair!
Trinity: Do you know what happened to Neo?
The Oracle: He is trapped in a place between this world and the machine world. All I can do is tell you that your friend needs your help. He needs all our help.
[war has ended]
Morpheus: I have imagined this moment for a long time. Is it real?
Councillor Dillard: Commander, do you think that we have any chance of survivng?
Lock: If I were you Councilor, I wouldn't ask me that question.
[looks to Morpheus]
Lock: I would ask him.
Councillor Dillard: Why?
Lock: Because *he's* the one that believes in miracles.
Mifune: What's a pod-born pencil-neck like you doing volunteering for my corps?
Kid: Neo, I believe.
[about the good luck charm]
Zee: You wore it.
Link: Are you kidding? I'll never take it off.
Trinity: [into intercom] Neo! It's Bane! He's psychotic!
[first lines]
AK: I got nothing, sir. No sign of Niobe or Ghost. Nothin' but blue pills.
[as the Hammer speeds through the mechanical line]
Morpheus: There's the exit.
Niobe: On my mark, give me full power, ninety degrees to lower left starboard.
Morpheus: Full power, ninety degrees...
[the ship approaches the exit... ]
Niobe: Now!
[... and she pulls it through a tight turn]
Niobe: Hold, on baby!
[the ship crashes through the exit, grinding to a halt]
Roland: God *damn*, woman, you can drive!
Roland: 'Bout time we had some goddamned good news...
First Operator at Command: Commander Lock, I got incoming.
Lock: We got a *dock* full of incoming!
Neo: Three lines...
Trinity: Power lines.
Neo: Follow them.
Mifune: What the shit is goin on over here?
[as the Hammer heads for Zion]
Lock's Lieutenant: Sir, their EMP could take out every sentinel up there.
Lock: It'll take out more than that. It'll wipe out our entire defense system. We blow an EMP inside there, we'll lose the dock.
Lock's Lieutenant: Sir, we *already* lost the dock.
Trinity: Do it, Neo.
Bane/Agent Smith: Yes, Shoot. Kill us. Fry us. Burn us alive.
Bane: What's that for?
Maggie: To help you relax. To make it easier for you to remember.
Bane: What if I don't want to remember?
Maggie: Why would you want that?
Bane: What if I blew that EMP? What if I did destroy those ships and I am responsible for the deaths of all those men? If I did that, it wouldn't be very safe for me here, would it?
[Bane stabs her]
Bane: Of course, it might not be very safe for you, either.