The Matrix Revolutions

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The Matrix Revolutions is a 2003 science fiction film directed by the Wachowskis. The film follows up directly from the previous film (as it was filmed simultaneously with Reloaded) and depicts everything going to hell as the machines reach Zion, humanity's real-world stronghold. While Zion is under assault, Neo sets into motion a plan to confront Agent Smith and end the war altogether. This is generally considered to be the weakest of the three films, although it does still contain some worthwhile elements.

Tropes used in The Matrix Revolutions include:

Anyone Can Die: The focus of.
Arch Nemesis: Smith. It turns out his opposition to The Chosen One is Inherent in the System and necessary to provide balance to the Matrix.
Arc Words: Everything that has a beginning has an end.
Big Bad: Agent Smith.
Black Dude Dies First: Averted with Morpheus—in fact, he is ultimately the only one in the main Power Trio to survive the series.
Blind Seer: Neo, quite literally. Lampshaded by Bane/Smith.
The Chessmaster: The Oracle, the matronly counterpart to the Architect. The entire plot has been...at the very least, heavily influenced by her desire to unbalance the Architect's Plan.
Deus Est Machina: There is a Machine character in the film named "Deus Ex Machina".
Dramatic Gun Cock: Trinity does this, even though she's already in the middle of a Mexican Standoff.
Eat Me: Done twice. The Oracle and Neo both let Smith assimilate them in order to destroy him.
Enemy Mine: Smith's conquest of the Matrix went so far that Neo and the Machines were forced to work together in order to stop him. The Machines made a temporary truce with the rest of the Human forces during this unrest. Smith got beaten and the Machines made their part and stopped all operations on the humans.
Epic Movie: The film goes this route, complete with a journey into the Machine City and a messianic ascension. The chief tune on the soundtrack is titled "Neodammerung", for Neo's sake!
Evil Cannot Comprehend Good: "Why, Mister Anderson, why, why do you persist?!"
Evil Counterpart: Smith to Neo, according to the Oracle.
Evil Laugh: Agent Smith after absorbing the Oracle, representing the randomness he gains.
Eye Scream: A fight between Neo and Bane/Smith. When the EMP beam goes awry and cuts a power cable, Smith jams it into Neo's face effectively melting his eyes.

Neo: I think you better drive.

First Time in the Sun: Trinity gets a nice eyeful of sunshine right before she dies.
Forbidden Zone: The Machine City, pretty much literally.
Gainax Ending: Arguable, but it is pretty strange.
Grand Theft Me: Poor Bane. While everybody else that Smith copies himself over is restored after Smith is finally beaten, Bane gets decapitated.
Groin Attack: Neo to Bane!Smith just before knocking his head off.
Hannibal Lecture: Smith loves these; his speech at the end is a brilliant Nietzsche Wannabe spiel. In return, Neo delivers a famous Shut UP, Hannibal in the train station scene; see Do Not Call Me "Paul".
Heroic Sacrifice: Neo.
Instant Awesome, Just Add Mecha: Why are there APU's defending the dock? Because they look frekkin Badass obviously!
Kudzu Plot: Compare the number of characters and plot points introduced in Reloaded to those followed up on in Revolutions.
Kung Fu Sonic Boom: During the final fight.
Last Stand: The Battle of Zion essentially amounts to this. With special mention to Cpt. Mifune's. The scene is even titled, "Mifune's Last Stand"
Long Game: The entire series can be described as a very long conflict between the Oracle and the Architect if you break things down enough. The Architect's first line to the Oracle near the end essentially drops the trope name.
Matrix-Healing Wave: The outcome of Neo's fight with Smith.
Mechanical Lifeforms: The Reveal at the end of the film that the machines have adapted to normal life on the (destroyed by humans) surface.
Melee a Trois: The last two movies were simply an all-out war between the Humans, who were fighting for survival as well for liberation from the Matrix, the Machines, who tries to destroy the Human race before they become too many to handle, and Smith, who had created his own clone army and wants to conquer both the Matrix and the real world.
- Not to mention various groups of programs exiled from the Machine world that appear as supernatural creatures within the Matrix.
Me's a Crowd: Smith's power.
The Mole: Bane (Via Deal with the Devil and Demonic Possession, respectively).
Mordor: The Machine City. Neo must make a seemingly-hopeless journey there at the climax.
Neck Snap: Morpheus uses this to kill a mook guarding an elevator.
Nice Job Fixing It, Villain: If Smith had simply beaten Neo to death, he would have won, but he chose to download himself into Neo instead. The symbolism aside (and there's a lot of it,) the literal interpretation of what's going on is that Smith doesn't realize Neo is jacked into the Matrix in the machine city, which means he's just connected himself to the Source, so the machines promptly delete him.
Nietzsche Wannabe: Agent Smith goes into a long rant about why Neo bothers to continue fighting him and that "Only a human mind could come up with something as insipid as love!" and "Why, Mr. Anderson!? Why!? Why do you persist!?" Ironically, Neo's response is something a Nietzschean Ubermensch might actually say: "Because I choose to."
The Nth Doctor: The Oracle is played by a different actress due to her original actress dying before completing her scenes; fortunately the directors were already toying with the idea of her changing "skins".
Oh Crap: Smith as he's finally overcome.

Smith: Oh no no no no no... No, it's not fair.

Omnicidal Maniac: (Agent) Smith has spread through the entire Matrix, already taken control of at least one person in the real world, and is poised to continue through to the Source mainframe and Machine City along with it - leading to the trilogy's concluding peace deal between the humans and the machines.

Smith: The purpose of all life...is to end.

Precision F-Strike:

The Oracle: You are a bastard.
Smith: You would know, Mom.

Really Seventeen Years Old: The Kid tries to say he's eighteen and gets laughed at. He convinces Mifune to let him help the corps anyway, though.
Rescued From Purgatory: Neo.
Screw Destiny: The focus of the movie.
Screaming Warrior: Where Mifune becomes the poster child of this trope.
Series Fauxnale: Was originally intended as the end of the film series.
Shining City: The Machine City from Neo's (blind) perspective.
Significant Anagram: The train station sign Mobil <=> Limbo, as mocked by Rifftrax.
Slow Electricity: Inside the Oracle's apartment building, the overhead lights go off, making clunking sounds, as a warning of Agent Smith's approach.
Synchronized Swarming: The swarming Sentinels make a hand-like shape. Later, robots form a face and it talks to Neo.
Technicolor Death: The explosive death/destruction of all of the Smiths.
This Thing You Call Love: Subverted by the programs, who Neo finds out are sentient and capable of love. Like our own Advertisement Server, for instance.
Throat Light: Happens briefly to Neo at the end as the machines channel their power through him to destroy the Agents Smith.
Tomato Surprise: The Reveal in the first film; Neo's machine-powers in the third.
Took a Level in Badass: Smith became the ruler of the Matrix.
Unnecessary Combat Roll: Morpheus, Trinity, and Seraph get into a fight with some guys who can bend gravity. Said guys do things like cartwheeling on the ceiling from cover to cover. They die.
Villainous Breakdown: Smith seemed to suffer from it in the final fight. He started out cool and collected if slighty cocky, but as the fight against Neo progressed, you can clearly see that Neo's tenacity slowly started to get to Smith. In his "Why do you persist?!" moment, he pretty much screams out his infamous rant with an enraged look in his eyes. When Neo answers his question ("Because I choose to"), Smith pretty much loses it.
The Virus: Smith, quite literally.
Walk Into Mordor: Well, after their vehicle crashes from catapulting above the cloud cover to avoid the giant robotic barrier monsters in the climax of the third film. Subverted by the fact that there seems to be a Yellow Brick Road of sorts composed of conspicuously well-lit power cables between the people-farms and the Machine City. But this plotline seems curiously informed by the Trope Namer, so...
Welcome to The Real World: More-or-less stated, but not actually an example of the trope.
What Is This Thing You Call Love?: Rama-Kandra and his wife actively love each other, culminating in "giving birth" to a new program, Sati.
The World Is Just Awesome: When Neo and Trinity break through the cloud cover and become the first humans (well, Trinity anyway) in centuries to see the sky, the sun, and the moon.
Yin-Yang Clash: Neo vs. Agent Smith.
You Can't Fight Fate: The last battle between Neo and Smith where Smith tries to persuade Neo to give up because it is pointless to keep fighting. Neo eventually gives up, but not just for Smith's reasons.
You Have No Chance to Survive: Smith.

Smith: Why, Mr. Anderson? Why do you do it? 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?