Trapped in the Subway

After the Mjolnir rescues the crew of the Nebuchadnezzar, Neo and Bane remain unconscious in the ship’s medical bay. But Neo is elsewhere. Inside the Matrix, he is stranded in a subway station called Mobil Ave—a limbo between the digital world and the machine realm.

There, he meets a family of programs. A girl named Sati stands out. Her father explains that the Trainman, a rogue program under the Merovingian’s command, controls the station. When Neo tries to board a train with them, the Trainman intervenes, overpowering him and leaving him trapped.

A Dangerous Rescue

Meanwhile, Seraph reaches out to Morpheus and Trinity. On behalf of the Oracle, he warns them of Neo’s imprisonment. Together, they track down the Merovingian to Club Hel. The club is a fortress of vice, crawling with guards. After a violent confrontation, they force the Merovingian to release Neo.

Freed at last, Neo seeks out the Oracle. She warns him of Smith’s growing power. The rogue program has a singular goal: the destruction of both the Matrix and the real world. Before departing, she tells Neo something ominous—“Everything that has a beginning has an end.”

After Neo leaves, Smith arrives with his swarm of clones. The Oracle does not resist. He assimilates her, absorbing her abilities. Now, Smith can see the future.

A Plan for Survival

In the real world, the crews of the Mjolnir and Nebuchadnezzar locate Niobe’s ship, the Logos, and bring it back online. They interrogate Bane, but he feigns amnesia, hiding the truth—Smith controls him now.

As Zion’s captains discuss defense strategies, Neo requests a ship. He must go to the Machine City. Niobe, moved by her own encounter with the Oracle, gives him the Logos. Trinity insists on joining him.

As they depart, Bane reveals himself. He has hidden aboard the ship. He captures Trinity and attacks Neo. In the struggle, Bane sears Neo’s eyes with a power cable, blinding him. But Neo discovers something new—he can see the machines in their purest form, glowing outlines of code. Using this ability, he kills Bane.

With Trinity at his side, he resumes course for the Machine City.

The Battle for Zion

Meanwhile, Morpheus and Niobe race toward Zion in the Mjolnir. The city is under siege. Thousands of Sentinels swarm the human defenses. Captain Mifune, leading the fight, falls in battle, but with his last breath, he orders the Kid to open the gate for the incoming ship. With the help of Zee, he succeeds.

The Mjolnir crashes into Zion’s dock, discharging an EMP blast. The Sentinels drop. But the victory comes at a cost. The pulse also disables Zion’s defenses. With no weapons left, the humans can only wait for the next wave. They believe the end has come.

The Last Journey

The Logos reaches Machine City but is met with a barrage of Sentinels. To escape, Trinity takes the ship to the sky, piercing the black clouds. For the first time in centuries, she and Neo witness the sun. But the moment is fleeting. The ship plummets back to Earth, crashing into a machine tower. Trinity is mortally wounded. With her dying breath, she says goodbye to Neo.

Alone, Neo presses forward. He reaches the heart of Machine City and meets the vast intelligence governing it—the Deus Ex Machina.

Neo presents a deal. Smith threatens not only the Matrix but also the machines themselves. If they allow Neo to face him, Zion will be spared. The machines agree. The Sentinels halt their attack.

The machines jack Neo into the Matrix one final time.

The Final Battle

The Matrix is a wasteland. Every inhabitant has been assimilated by Smith. Now, only one remains—Smith himself, standing in the Oracle’s form. He welcomes Neo with confidence. He has seen the future, and in it, he wins.

The battle begins. They clash in the pouring rain, the city crumbling around them. Punches land with the force of explosions. They soar through the air, striking and countering. Neo fights with everything he has. But Smith is relentless. He keeps coming back.

Then, Smith speaks the Oracle’s words: “Everything that has a beginning has an end.”

Neo understands. He stops fighting. He lets Smith assimilate him.

A blinding surge of energy erupts. In the real world, the machines flood Neo’s body with power. Inside the Matrix, the result is devastating. The Smith-Neo entity convulses and collapses. The virus spreads in reverse. Every Smith is deleted. The Oracle is freed. The Matrix is saved.

Neo’s body goes still. The war is over.

A New Era

The Sentinels withdraw from Zion. The survivors embrace, realizing the impossible has happened. The battle has ended not with destruction, but with peace.

Neo’s body is taken away by the machines, his fate unknown.

In the rebooted Matrix, the Oracle meets the Architect. They agree that the peace will last as long as it can. Those who wish to leave the simulation will be allowed to do so. Sati, the girl Neo met in the subway, watches the sky change, painting it with colors in Neo’s honor.

Seraph asks the Oracle if she knew how it would end. She smiles. “I didn’t know,” she says. “I believed.”