The Matrix Revolutions
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 ends up 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 and Trinity is viciously killed by being impaled by metal rebar.