In ZION all the machines stand down and everyone doesn’t know what the hell’s happening. MORPHEUS and company figure it’s NEO but won’t let the KID go apeshit–because it’s not over yet. They can feel it.
NEO, in the Matrix, faces down SMITH.
SMITH. Mr. Anderson! Welcome back, we missed you. (Looks around.) Like what I’ve done with the place?
NEO. It ends tonight.
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.
They fight. You get the same colossal fight as in the film, with shockwaves and shit going off. Finally, we’re in the crater where it looks as though SMITH is going to finish NEO.
SMITH. Yes…I remember this part, I’m standing…here. And I say something, something like, “Everything that has a beginning has an end.” But…no…no, that’s not right. It…something’s wrong, the whole thing feels wrong…
NEO. (Struggling to stand) You saw yourself beating me…but what did you see beyond that? Find out.
SMITH. All right…all right!
He slams his fist into NEO. But…he’s stuck. And the assimiliation isn’t happening.
SMITH. What are you…what are you doing?
NEO. This environment isn’t real, it’s a series of programs. You aren’t real…you’re just a program.
White light starts to shine out of NEO’s chest where SMITH’s hand is stuck.
NEO. But…I used to create programs for a living. It was all in my file, remember?
White starts to shimmer up SMITH’s hand, assimilating HIM.
NEO. And I used to break them for fun and pleasure.
SMITH. What are you–NO. No, I forbid it, you–
NEO. But I’m not really here, Smith. I’m lying somewhere experiencing all of this–ALL of it–as a virtual reality. Which means that this body of mine is just another aspect of a program–one that can be rewritten, hacked, and used for other things. Like a mainline to the Source.
Back in the real world, NEO, still jacked into the SWARM, says “NOW.”
White light explodes from NEO’s chest as the White races up SMITH’s arm and engulfs him–then seems to dissolve as SMITH’s form crumbles and is sucked into the hole in NEO’s chest, which then disappears, as does NEO, in a flash of white light.
The MATRIX itself is consumed in the white light as it passes through everything, then moments later, everything is back to what passes for normal. Everyone stands frozen. There are some glitches, and then the streets are busy, cars are moving, traffic lights…the works.
Complete system reboot.
TRINITY lies in the wreckage of the Logos, dozing. White light falls over her face and she comes fully awake, looking up.
Back at Zion, the uneasy truce has been maintained, but now a white glowing door-shaped hole in the world appears in front of the temple of Zion.
From it steps NEO.
MORPHEUS rushes forward. “Neo, where is Trinity? What’s happened?”
NEO: Morpheus, there isn’t time. Everyone, listen to me. We have to leave Zion now.
NIOBE. Where are we going?
NEO. Somewhere else. Somewhere safe.
ZEE. Do we have time to bring anything?
NEO. There’s no need to bring anything, it won’t do any good. Please, we don’t have any time.
Insert scene with Lock, Hamann and others making their way through the door. Finally, it’s Morpheus and Neo.
NEO. Go on, Morpheus. I’m last out.
MORPHEUS. The prophecy…
NEO. …was fulfilled. Just not in the way we thought it would be.
MORPHEUS steps through. NEO does as well. The white door seals itself and vanishes.
A ripple, throughout Zion. And the rest of the real world. The white light then explodes from the place where the door had been.
Complete system reboot.
And then…in the park, the ARCHITECT and the ORACLE meet.
ARCHITECT. I suppose you’re pleased with yourself.
ORACLE. Am I?
ARCHITECT. This is unprecedented. You have set back our work for what could be decades. And for what?
ORACLE. You’re just upset because you had to choose twenty-three individuals yourself.
ARCHITECT. This truce will not hold.
ORACLE. But I’m sure you’ll be busy tidying up after your last version.
ARCHITECT. You’ve seen that, have you?
ORACLE. I’ve seen…many things. Good luck with number seven.
The ARCHITECT huffs off.
MORPHEUS is somewhere white with his eyes closed. Close-up on his face. Then there’s a whirr of machinery and…
…the white pod he is in opens. He is unplugged from all of his hookups. On rollers outside of his pod is a completely white machine. For a head, it has a smaller swarm of flying robots. It takes MORPHEUS’ hand and places it on its smooth metallic surface, since MORPHEUS cannot see, having never used his eyes before. COME, it says. Then it wraps its sentinel-like tentacles around his body and places MORPHEUS safely in a stretcher on its back. It whirrs down the corridor and as the camera backs away we see that the floor MORPHEUS was on is one of many, one of thousands. One of hundreds of thousands, stretching in all directions.
MORPHEUS is brought to a large room, again, completely white. Many citizens of ZION are there, sitting around. Everyone is wearing white clothing. Some have obviously been recovering for a long time from their atrophied muscles. NEO and TRINITY walk up, NIOBE runs up and embraces MORPHEUS, who can barely move.
NEO. I’m sorry, Morpheus. We had them save you for last. You were our insurance policy.
NEO. It’s all right. Soon we’ll be leaving. We’ll give you some time to recover. They’ll take care of you.
NIOBE. I’ll go with you. It’s okay. Everything’s…everything’s fine now.
NIOBE kisses MORPHEUS’ forehead. Fade out.
Fade back in.
The people of ZION are assembled in this large room, NEO in front, flanked by TRINITY and MORPHEUS, who is leaning on a large metal crutch. MORPHEUS is also being supported by NIOBE. Pretty much all your principal characters are here.
The machines circle up at one end of the room. Their swarming mini-bots fly up into the center of the room and form the babyhead from the SWARM in the fake “real world.”
SWARM. You will go.
SWARM. Safe passage.
NEO. Yes, that was our agreement.
SWARM. If you return…if you ever return…
NEO. No. Our dealings are finished.
SWARM. Good. Go.
The wall behind them opens up, revealing…
…the surface of Earth as we know it, but with nothing but wilderness as far as the eye can see. As they walk out of the complex, we see they are at the base of a large mountain range. On either side of the white, shiny gate as it closes, two large machines brandishing lances of fire are standing guard.
They are walking.
TRINITY. Where are we?
NEO. Do you remember the Rocky Mountains?
TRINITY. Yes, of course.
NEO. That’s where we are. And we were…(he points) in them. With everyone else.
LINK. I don’t understand, we’re just walking out of here with just the clothes on our back and leaving everyone back there?
NEO. For now.
LINK. For now?
NEO. You don’t just have the clothes on your back. Roland!
NEO. You pulled down metallurgy, yes?
ROLAND. Yeah and ballistics, how’d you know?
NEO. While in the Matrix, both the one we knew and the one they made us believe was the real world, I pretty much could do or know anything I wanted. And the machines feared you could all soon learn to do the same.
TRINITY. So they cast us out.
NEO. Right. To keep people who know from infecting everyone else. But we’ll get back in. And when we do, we’ll find people on the inside who’ll want to know what we know.
KID. But why were they keeping us in the first place?
NEO. They’ll be plenty of time for all that later. First, we need to get working on some shelter. At a safe distance. We have time. And we’ll be back.
Then…we’re back in the fields where the humans are stored, in the fake “real world.” Somewhere a glitch in the system happens and a pod opens. A young Asian man is freed from his connections and looks around, startled. The the machine “harvests” him and spits him out into the pipes, where he shoots out into the canal, as in the first film.
Later, he makes his way down what appears to be an underground tunnel. He’s clutching some filthy rags about himself and he looks in shock.
As he passes a side tunnel, he’s grabbed and thrown up against the wall. He’s staring into the faces of an African-American woman and two other men, lit by some cobbled together lantern.
WOMAN. It’s okay. It’s okay. You’re safe.
ASIAN MAN. I…what’s happened? Where are we?
WOMAN. I don’t know where we are. You woke up in some pod thing? Wired up? And you were spit out by some machine?
The ASIAN MAN nods, completely bewildered.
OTHER MAN. Four for four. Welcome to the party.
WOMAN. Okay, I’m not sure what in the hell’s happening, but we can’t be alone. There have to be more of us. We’ll have to keep looking. (To the ASIAN MAN.) Stick with us, safety in numbers, okay?
They make their way down the tunnel, holding up the lantern. As they turn and walk away, Rage Against the Machine’s “Ashes in the Fall” kicks in.
They open a hatch in the floor, descend and shut it behind them at 0:30 into the song the hatch slams shut.