The Matrix Revolutions
When Neo wakes up, he finds himself at a train station. He is there because, when he used his power to destroy the sentinels at the end of the second movie, he touched the source and did not come back all the way. He is stuck there. Meanwhile, his girlfriend Trinity, Morpheus, and Seraph enter a club to talk to the Merovingian, who controls a lot of the Matrix. A gun fight ends in a Mexican standoff with guns pointed towards everyone. The Merovingian agrees to let Neo go, and Trinity picks him up.
The city of Zion is preparing for war. They pool all of their resources into a dock area. They use Armored Personnel Units (APU) to fight back. However, there are too many machines, and they soon have to fall back to the temple.
Niobe on her ship attempts to return to Zion by going through an area that only a very skilled pilot can go through. However, Niobe makes a mistake and the machines come after them. During one part of the dock battle, the commander Milfune tries to repel the machines but is overwhelmed. He dies. He tells the Kid to take his APU and to open the dock doors. The Kid does so and the ship comes through, blows its EMP, and saves the dock for now.
Near the end of the movie, Neo wants to take a ship to talk directly to the machines. Niobe turns her ship, the Logos, over to him. Earlier, Bane (who is now Smith) had stabbed a crew member and hid away on the Logos. While on the ship, Bane fights Neo and burn his eyes out. However, Neo has the power and can still see and kills Bane. As Neo and Trinity approach, the machines attack. Trinity flies above the clouds to kill the machines, but it also destroys their engines, and they lose control and crash into the ground, killing Trinity.
Neo walks up to the head of the machines, whose name is Deus Ex Machina. He says that Smith has gotten out of control and that he is the only one that can stop him. He says that he wants peace, so the machines stop attacking Zion. Neo and Smith start fighting again. This time Neo cannot beat him like he did with Bane. At the end, he says, "It was inevitable" and allows Smith to touch him and acquire him. Smith is then destroyed, as his only purpose was to balance Neo, who is now gone.