The Showdown in Mega City was the epic conclusion of the Machine War manifested as a final confrontation between Neo and the viral Smith. Faced with an onslaught of Smith clones and a nigh-omnipotent Smith, who has absorbed the Oracle and her premonitions, Neo eventually finds himself outmatched, but accomplishes a miraculous feat that not even Smith foresaw.
Journey to the Machine City
What do you want?"”
― Deus Ex Machina and Neo[src]
The Oracle has warned Neo of Smith's burgeoning presence in the Matrix. She says that the end of the war is coming no matter what. As the Resistance makes their final stand for Zion, a blinded Neo and Trinity fly to the Machine City in Niobe's ship, the Logos.
Once arriving to the Machine City, many Sentinels begin to chase and attack the hovercraft using their laser and tow bomb capabilities. Neo, using the powers of The One, is able to destroy all incoming sentinels and weapons coming their way.
As Neo's powers were still no match for the hoard of Sentinels charging towards their ship, Neo orders Trinity to fly upward to avoid them. As the hovercraft moved more upward towards sunlight, the Sentinels around the Logos begin to lose power and fall after coming into contact with the sunlight. Still flying upward, the Logos finally flies beyond the clouds and Neo and Trinity witness the shining sun. After a short moment of happiness, the Logos begins to descend down into the dark atmosphere of the Machine City.
As they descend, Neo can see that they are close to their destination. Neo then orders Trinity to pump the ignitor to restart the ship. After a few attempts, the engine beings to fully function but not before the hovercraft rapidly soars downward, crashing the Logos into the structure. As the hovercraft crashed, metallic spikes attached to the structure travels through the hovercraft and three spikes managed to impale Trinity through her chest.
After Neo and Trinity realized they were alive, Neo found Trinity and told her that they survived and that they finally made it. However, Trinity told Neo that she will not be able to go with him to the end as she knows that her journey as ended. Neo feels her body and touches one of the spikes that impaled her and realized what has happened. As Trinity tells Neo that everything was going to be alright, Neo begins to cry and tells her that he cannot fulfill his destiny without her.
Trinity tells Neo he can and she tells him about her love for him before she dies. Neo says goodbye to her and crawls out of the Logos to make his say once and for all.
Neo walks to the near top of the structure and stands near the edge of an ending platform. Moments later, the machine king, Deus Ex Machina, appears to him and tells him to speak his purpose. Neo insists that Smith has become too powerful and he will soon conquer the Real World when he is through with conquering the Matrix.
The two make a bargain: if Neo can destroy Smith, the Machines will make peace with Zion and the Resistance. Deus Ex Machina provides Neo with an uplink to jack in to the Matrix. Before Neo enters the Matrix, he vows that he will not fail.
Neo finds himself walking along a street in Mega City through a torrent of rain. Alongside him and in the buildings above have gathered thousands of Smith clones, sneering and scowling at Neo as he passes. Up ahead the Smith who has absorbed the Oracle steps into the street to face Neo. They exchange their acknowledgment that it will all end here and now, with Smith asserting that he will be victorious, having seen the outcome of their skirmish. Clenching their fists, the two combatants begin racing toward each other. The battle for the fate of the Matrix is underway.
It ends tonight."”
"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 I'm the one that beats you!
― Neo and Smith[src]
When they meet, the fight starts out in Neo's favor. Smith throws a punch at Neo but Neo quickly blocks it with a reverse axe kick. Then Neo and Smith begin to exchange different attacks at one another with both of them blocking and counterattacking one another. Neo's combat abilities still seem to outshine Smith's as he avoids Smith's blows while landing his own. Finally, they simultaneously land hard right hooks on the other and are both sent flying away from each other.
Neo lands lightly on his feet, but Smith lands on his back making an indented skid along the road. An angry Smith then takes to the sky and Neo follows. They clash spectacularly in midair sending a wave of water down on the watching Smith clones below. Rolling over and over in the air, they exchange punches and headbutts and Smith throws Neo into a nearby building, where Neo smashes through a couple of walls.
Neo stands and Smith rockets through the openings in pursuit. Neo deftly leaps over Smith who pauses in midair awaiting Neo's move. Neo kicks off from the wall and charges Smith. Once again, they collide and fly backwards, both enduring hard falls. Neo is slower to get up than Smith, who taunts Neo with his impending demise. Refusing to relent, Neo takes a stance and beckons Smith to come. An infuriated Smith rushes towards Neo and their battle resumes.
Smith comes with a fast flurry of punches, but Neo is faster, knocking Smith back and delivering a brutal series of kicks to Smith's face. Neo then lands one tremendous kick sending Smith smashing through the window and flying backwards through the air for some distance.
Smith speeds back towards Neo where they collide in midair once more. Grappling and brawling with each other, they rise higher and higher in the air against great flashes of lightning. Both land impressive blows on the other until Smith chooses to loop around and charge Neo after being knocked backward. Neo chooses to steel himself against Smith's charge, but is knocked out of the air.
Smith takes advantage of this by grabbing Neo and careening at full speed towards the ground in a devastating pile-driver. The impact of Smith's thunderous attack creates a monumental wave of impact and creates a huge crater in the street with Smith standing over a beaten and exhausted Neo.
As the rain continues to pour, the Smith clones gather around the impact crater to watch. As the seemingly unbeatable Smith stands over his opponent, Neo stirs and slowly gets on all fours to get up and continue fighting. Almost at a loss, Smith begins to question the reasoning behind Neo's actions with rising fury.
Smith ardently makes the claim that Neo's plight is meaningless and nothing he fights for carries any significance, especially in the face of the impossibility of him winning. Furthermore, Smith disparages human sentiment and intellect and compares their artificiality to the Matrix. Neo simply replies that it is his choice to keep fighting.
Smith once again throws a series of punches at Neo, who vaguely blocks and parries them, after which he throws a walloping right hook, which actually dizzies Smith for a moment. Neo then delivers a straight arm to Smith's chest, burying him in the rubble, but Neo is clearly spent of his energy. Smith bursts forth from the rubble and flies into Neo, tackling him to the ground. Smith beats Neo in the face, then lifts him up and punches him backwards. Neo lands on the ground, not getting up.
All at once, Smith realizes that having absorbed the Oracle, he has foreseen this happening and is supposedly meant to say something. The words that come out are, "everything that has a beginning has an end, Neo." Neo looks at Smith, who winces, shocked at what he said. Believing he has been subverted, Smith questions the reality of his behavior. Neo gets up and a panicked Smith backs away.
Neo surrenders to Smith, agreeing that it was always "inevitable". Growing more unnerved, Smith jams his palm into Neo's chest and Neo allows himself to be copied over by Smith. When his assimilation is complete and a new Smith stands in his place, Smith nervously asks, "is it over?" The new clone nods.
It is done.”
― Deus Ex Machina[src]
Back in Machine City, Neo's plugin device sends a shock through his body and the new clone jolts. Rays of golden light shoot forth from Neo and his assimilated self in the Matrix. The Machines are able to send a deletion program through Neo into the Matrix. Smith stares in horror as the clone explodes in a flash of light, followed by his many other clones and then himself.
After Smith and all of his clones were destroyed, the Oracle's body returned to the Matrix and reloaded into the puddle on the bottom of the crater where Neo and Smith confronted during their duel and all those who were assimilated by Smith returned back to their normal selves in the Matrix.
A New Start
Just how long do you think this peace is going to last?"”
"As long as it can.
― The Architect and The Oracle[src]
After Smith's destruction, the plugin cables retreat gently from Neo's corpse. The Sentinels retreat from Zion leaving the humans at truce. Kid realizes that the Sentinels were retreating and knew that Neo saved them all and ended the war. He then ran round Zion screaming that Neo ended the war and everything was over. Kid eventually reached the lower section of Zion, where the majority of the redpills were hiding during the battle for Zion, and screamed from the top platform that the war was finally over.
After his scream echoed throughout the area, all of the people within Zion began to cheer. The people within the lower area of Zion began to rejoice by hugging and kissing one another. Link and Zee gracefully kiss as they are grateful that the war is finally over.
Back near the docks, Lock is shocked by what is happening and Niobe hugs Morpheus while crying in his arm. Morpheus begins to cry as well as he tells Niobe that he has been dreaming of this day for so long. A day where after over a hundred years of fighting, there was peace.
Niobe, while still in Morpheus' arms, prayed and said that if Neo was out there listening to them somehow, she wanted to tell him thank you for all he has done and for saving all of humanity.
Back in the Machine City, Neo's body is given a respectful procession by the Machines and is taken away with them to another part in the Real World. Damage done by Smith is rewritten and the Matrix reboots with a new program.
Sati awakes with a black cat walking beside her and looks up into the new sky. Somewhere on the outskirts of Mega City, the Architect meets with the Oracle to discuss about the situation that is at hand with the humans and Machines.
The Architect asks sinisterly how long the peace with the humans and the Machines will last and the Oracle tells him however long it can and will. The Architect begins to leave and the Oracle asks him if he will keep his word and about the status of bluepills. The Architect tells her that the others are able to leave if they wish while this peace is still in agreement. Asking if she has his word on that, the Architect jokes and responds with, "What do you think I am? Human?".
After the Architect leaves, Sati and Seraph walk towards the Oracle to join her and Sati shows how happy she is now that the world is at peace. She then uses her powers to summon the sun and have it shine down on Mega City. Sati tells the Oracle that the sun is in honor for Neo and she then asks the Oracle if he will ever return.
The Oracle replies to Sati that maybe someday Neo will return and they will see him once again. Seraph then asked the Oracle if she always knew that this day would come. The Oracle tells him that she didn't always know, but that she believed. Then the three stare into the shining sun as a new dawn is arising within the Matrix and the world is no long limited to anyone.